Load data

Per-well profiles computed in single_cell_analysis are loaded, as well as metadata associated with these profiles (obtained from BBBC021)

# profiles <-
#   readr::read_csv(system.file("extdata", "ljosa_jbiomolscreen_2013_per_well_mean.csv",
#                 package = "cytominergallery"))

profiles <-
 readr::read_csv("~/work/projects/dp_treatment-classification_az/workspace/backend/ljosa_2013_skopy/ljosa_2013_skopy_aggregated.csv")

moa <-
  readr::read_csv(system.file("extdata", "BBBC021_v1_moa.csv",
                              package = "cytominergallery")) %>%
  rename(Image_Metadata_Compound = compound,
                Image_Metadata_Concentration = concentration,
                Image_Metadata_MoA = moa
  )

metadata <-
  readr::read_csv(system.file("extdata", "BBBC021_v1_image.csv",
                              package = "cytominergallery")) %>%
  rename(Image_Metadata_Plate = Image_Metadata_Plate_DAPI,
                Image_Metadata_Well = Image_Metadata_Well_DAPI
  ) %>%
  select(matches("^Image_Metadata")) %>%
  inner_join(moa) %>%
  distinct()

profiles %<>%
  inner_join(metadata)

variables <-
  colnames(profiles) %>%
  str_subset("^Nuclei_|^Cells_|^Cytoplasm_")

How many compounds?

profiles %>%
  filter(Image_Metadata_Compound != "DMSO") %>%
  distinct(Image_Metadata_Compound) %>%
  tally() %>%
  rename(`Number of compounds` = n) %>%
  knitr::kable()

Number of compounds
38

How many unique treatments (compound-concentration pairs)?

profiles %>%
  filter(Image_Metadata_Compound != "DMSO") %>%
  distinct(Image_Metadata_Compound, Image_Metadata_Concentration) %>%
  tally() %>%
  rename(`Number of unique treatments` = n) %>%
  knitr::kable()

Number of unique treatments
103

How many replicates per unique treatment?

profiles %>%
  filter(Image_Metadata_Compound != "DMSO") %>%
  count(Image_Metadata_Compound, Image_Metadata_Concentration) %>%
  rename(`Number of replicates` = n) %>%
  knitr::kable()

Image_Metadata_Compound	Image_Metadata_Concentration	Number of replicates
ALLN	3.000	3
ALLN	100.000	3
alsterpaullone	1.000	2
alsterpaullone	3.000	2
anisomycin	0.300	3
anisomycin	1.000	3
AZ-A	0.100	3
AZ-A	0.300	3
AZ-A	1.000	3
AZ-A	3.000	3
AZ-A	10.000	3
AZ-A	30.000	3
AZ-C	0.001	3
AZ-C	0.003	3
AZ-C	0.010	3
AZ-C	0.030	3
AZ-C	0.100	3
AZ-C	0.300	3
AZ-C	1.000	3
AZ-J	1.000	3
AZ-J	3.000	3
AZ-J	10.000	3
AZ-U	1.000	3
AZ-U	3.000	3
AZ-U	10.000	3
AZ138	0.030	3
AZ138	0.100	3
AZ138	0.300	3
AZ138	1.000	3
AZ138	3.000	3
AZ258	0.100	3
AZ258	0.300	3
AZ258	1.000	3
AZ841	0.100	3
AZ841	0.300	3
AZ841	1.000	3
bryostatin	0.300	2
camptothecin	0.003	3
camptothecin	0.010	3
camptothecin	0.030	3
chlorambucil	10.000	3
cisplatin	10.000	3
colchicine	0.030	3
cyclohexamide	5.000	3
cyclohexamide	15.000	3
cyclohexamide	50.000	3
cytochalasin B	10.000	3
cytochalasin B	30.000	3
cytochalasin D	0.300	3
demecolcine	0.300	3
demecolcine	1.000	3
demecolcine	3.000	3
demecolcine	10.000	3
docetaxel	0.030	3
docetaxel	0.100	3
docetaxel	0.300	3
emetine	0.100	3
emetine	0.300	3
emetine	1.000	3
epothilone B	0.100	3
epothilone B	0.300	3
epothilone B	1.000	3
etoposide	1.000	3
etoposide	3.000	3
etoposide	10.000	3
floxuridine	10.000	3
floxuridine	30.000	3
lactacystin	10.000	3
latrunculin B	1.000	3
latrunculin B	3.000	3
methotrexate	10.000	3
mevinolin/lovastatin	1.500	3
mevinolin/lovastatin	5.000	3
mevinolin/lovastatin	15.000	3
MG-132	0.100	3
MG-132	3.000	3
mitomycin C	0.100	3
mitomycin C	0.300	3
mitomycin C	1.000	3
mitomycin C	3.000	3
mitoxantrone	0.003	3
mitoxantrone	0.010	3
nocodazole	1.000	3
nocodazole	3.000	3
PD-169316	3.000	2
PD-169316	10.000	2
PP-2	3.000	2
PP-2	10.000	2
proteasome inhibitor I	0.100	3
proteasome inhibitor I	3.000	3
simvastatin	2.000	3
simvastatin	6.000	3
simvastatin	20.000	3
taxol	0.300	3
taxol	1.000	3
taxol	3.000	3
vincristine	0.003	3
vincristine	0.010	3
vincristine	0.030	3
vincristine	0.100	3
vincristine	0.300	3
vincristine	1.000	3
vincristine	3.000	3

How many DMSO wells per plate?

profiles %>%
  filter(Image_Metadata_Compound == "DMSO") %>%
  count(Image_Metadata_Plate) %>%
  rename(`Number of DMSO wells` = n) %>%
  knitr::kable()

Image_Metadata_Plate	Number of DMSO wells
Week1_22123	6
Week1_22141	6
Week1_22161	6
Week1_22361	6
Week1_22381	6
Week1_22401	6
Week10_40111	6
Week10_40115	6
Week10_40119	6
Week2_24121	6
Week2_24141	6
Week2_24161	6
Week2_24361	6
Week2_24381	6
Week2_24401	6
Week3_25421	6
Week3_25441	6
Week3_25461	6
Week3_25681	6
Week3_25701	6
Week3_25721	6
Week4_27481	6
Week4_27521	6
Week4_27542	6
Week4_27801	6
Week4_27821	6
Week4_27861	6
Week5_28901	6
Week5_28921	6
Week5_28961	6
Week5_29301	6
Week5_29321	6
Week5_29341	6
Week6_31641	6
Week6_31661	6
Week6_31681	6
Week6_32061	6
Week6_32121	6
Week6_32161	6
Week7_34341	6
Week7_34381	6
Week7_34641	6
Week7_34661	6
Week7_34681	6
Week8_38203	6
Week8_38221	6
Week8_38241	6
Week8_38341	6
Week8_38342	6
Week9_39206	6
Week9_39221	6
Week9_39222	6
Week9_39282	6
Week9_39283	6
Week9_39301	6

Feature selection

Next, lets filter the set of features based on various measures of quality

Drop NA columns

profiles <-
  cytominer::variable_select(
    population = profiles,
    variables = variables,
    operation = "drop_na_columns"
)

## INFO [2018-02-05 14:39:04] excluded:
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_angular_second_moment_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_angular_second_moment_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_angular_second_moment_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_angular_second_moment_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_contrast_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_contrast_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_contrast_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_contrast_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_correlation_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_correlation_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_correlation_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_correlation_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_difference_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_difference_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_difference_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_difference_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_difference_variance_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_difference_variance_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_difference_variance_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_difference_variance_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_information_measure_of_correlation_1_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_information_measure_of_correlation_1_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_information_measure_of_correlation_1_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_information_measure_of_correlation_1_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_information_measure_of_correlation_2_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_information_measure_of_correlation_2_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_information_measure_of_correlation_2_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_information_measure_of_correlation_2_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_inverse_difference_moment_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_inverse_difference_moment_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_inverse_difference_moment_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_inverse_difference_moment_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_average_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_average_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_average_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_average_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_of_squares_variance_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_of_squares_variance_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_of_squares_variance_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_of_squares_variance_8_270
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_variance_8_000
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_variance_8_090
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_variance_8_180
## INFO [2018-02-05 14:39:04]    Cells_Actin_haralick_sum_variance_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_angular_second_moment_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_angular_second_moment_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_angular_second_moment_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_angular_second_moment_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_contrast_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_contrast_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_contrast_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_contrast_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_correlation_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_correlation_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_correlation_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_correlation_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_difference_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_difference_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_difference_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_difference_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_difference_variance_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_difference_variance_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_difference_variance_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_difference_variance_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_information_measure_of_correlation_1_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_information_measure_of_correlation_1_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_information_measure_of_correlation_1_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_information_measure_of_correlation_1_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_information_measure_of_correlation_2_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_information_measure_of_correlation_2_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_information_measure_of_correlation_2_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_information_measure_of_correlation_2_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_inverse_difference_moment_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_inverse_difference_moment_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_inverse_difference_moment_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_inverse_difference_moment_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_average_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_average_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_average_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_average_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_of_squares_variance_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_of_squares_variance_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_of_squares_variance_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_of_squares_variance_8_270
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_variance_8_000
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_variance_8_090
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_variance_8_180
## INFO [2018-02-05 14:39:04]    Cells_Tubulin_haralick_sum_variance_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_angular_second_moment_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_angular_second_moment_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_angular_second_moment_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_angular_second_moment_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_contrast_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_contrast_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_contrast_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_contrast_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_correlation_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_correlation_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_correlation_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_correlation_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_difference_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_difference_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_difference_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_difference_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_difference_variance_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_difference_variance_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_difference_variance_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_difference_variance_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_information_measure_of_correlation_1_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_information_measure_of_correlation_1_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_information_measure_of_correlation_1_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_information_measure_of_correlation_1_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_information_measure_of_correlation_2_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_information_measure_of_correlation_2_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_information_measure_of_correlation_2_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_information_measure_of_correlation_2_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_inverse_difference_moment_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_inverse_difference_moment_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_inverse_difference_moment_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_inverse_difference_moment_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_average_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_average_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_average_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_average_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_of_squares_variance_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_of_squares_variance_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_of_squares_variance_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_of_squares_variance_8_270
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_variance_8_000
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_variance_8_090
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_variance_8_180
## INFO [2018-02-05 14:39:04]    Cells_DAPI_haralick_sum_variance_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_angular_second_moment_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_angular_second_moment_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_angular_second_moment_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_angular_second_moment_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_contrast_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_contrast_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_contrast_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_contrast_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_correlation_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_correlation_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_correlation_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_correlation_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_difference_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_difference_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_difference_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_difference_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_difference_variance_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_difference_variance_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_difference_variance_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_difference_variance_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_information_measure_of_correlation_1_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_information_measure_of_correlation_1_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_information_measure_of_correlation_1_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_information_measure_of_correlation_1_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_information_measure_of_correlation_2_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_information_measure_of_correlation_2_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_information_measure_of_correlation_2_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_information_measure_of_correlation_2_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_inverse_difference_moment_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_inverse_difference_moment_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_inverse_difference_moment_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_inverse_difference_moment_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_average_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_average_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_average_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_average_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_of_squares_variance_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_of_squares_variance_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_of_squares_variance_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_of_squares_variance_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_variance_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_variance_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_variance_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Actin_haralick_sum_variance_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_angular_second_moment_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_angular_second_moment_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_angular_second_moment_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_angular_second_moment_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_contrast_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_contrast_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_contrast_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_contrast_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_correlation_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_correlation_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_correlation_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_correlation_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_difference_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_difference_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_difference_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_difference_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_difference_variance_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_difference_variance_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_difference_variance_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_difference_variance_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_information_measure_of_correlation_1_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_information_measure_of_correlation_1_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_information_measure_of_correlation_1_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_information_measure_of_correlation_1_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_information_measure_of_correlation_2_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_information_measure_of_correlation_2_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_information_measure_of_correlation_2_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_information_measure_of_correlation_2_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_inverse_difference_moment_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_inverse_difference_moment_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_inverse_difference_moment_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_inverse_difference_moment_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_average_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_average_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_average_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_average_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_of_squares_variance_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_of_squares_variance_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_of_squares_variance_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_of_squares_variance_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_variance_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_variance_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_variance_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_Tubulin_haralick_sum_variance_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_angular_second_moment_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_angular_second_moment_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_angular_second_moment_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_angular_second_moment_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_contrast_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_contrast_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_contrast_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_contrast_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_correlation_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_correlation_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_correlation_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_correlation_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_difference_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_difference_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_difference_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_difference_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_difference_variance_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_difference_variance_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_difference_variance_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_difference_variance_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_information_measure_of_correlation_1_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_information_measure_of_correlation_1_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_information_measure_of_correlation_1_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_information_measure_of_correlation_1_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_information_measure_of_correlation_2_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_information_measure_of_correlation_2_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_information_measure_of_correlation_2_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_information_measure_of_correlation_2_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_inverse_difference_moment_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_inverse_difference_moment_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_inverse_difference_moment_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_inverse_difference_moment_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_average_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_average_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_average_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_average_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_entropy_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_entropy_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_entropy_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_entropy_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_of_squares_variance_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_of_squares_variance_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_of_squares_variance_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_of_squares_variance_8_270
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_variance_8_000
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_variance_8_090
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_variance_8_180
## INFO [2018-02-05 14:39:04]    Cytoplasm_DAPI_haralick_sum_variance_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_angular_second_moment_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_angular_second_moment_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_angular_second_moment_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_angular_second_moment_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_contrast_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_contrast_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_contrast_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_contrast_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_correlation_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_correlation_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_correlation_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_correlation_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_difference_entropy_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_difference_entropy_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_difference_entropy_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_difference_entropy_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_difference_variance_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_difference_variance_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_difference_variance_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_difference_variance_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_entropy_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_entropy_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_entropy_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_entropy_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_information_measure_of_correlation_1_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_information_measure_of_correlation_1_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_information_measure_of_correlation_1_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_information_measure_of_correlation_1_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_information_measure_of_correlation_2_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_information_measure_of_correlation_2_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_information_measure_of_correlation_2_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_information_measure_of_correlation_2_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_inverse_difference_moment_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_inverse_difference_moment_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_inverse_difference_moment_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_inverse_difference_moment_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_average_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_average_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_average_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_average_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_entropy_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_entropy_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_entropy_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_entropy_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_of_squares_variance_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_of_squares_variance_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_of_squares_variance_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_of_squares_variance_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_variance_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_variance_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_variance_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Actin_haralick_sum_variance_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_angular_second_moment_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_angular_second_moment_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_angular_second_moment_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_angular_second_moment_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_contrast_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_contrast_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_contrast_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_contrast_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_correlation_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_correlation_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_correlation_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_correlation_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_difference_entropy_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_difference_entropy_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_difference_entropy_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_difference_entropy_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_difference_variance_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_difference_variance_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_difference_variance_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_difference_variance_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_entropy_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_entropy_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_entropy_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_entropy_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_information_measure_of_correlation_1_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_information_measure_of_correlation_1_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_information_measure_of_correlation_1_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_information_measure_of_correlation_1_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_information_measure_of_correlation_2_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_information_measure_of_correlation_2_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_information_measure_of_correlation_2_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_information_measure_of_correlation_2_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_inverse_difference_moment_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_inverse_difference_moment_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_inverse_difference_moment_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_inverse_difference_moment_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_average_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_average_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_average_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_average_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_entropy_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_entropy_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_entropy_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_entropy_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_of_squares_variance_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_of_squares_variance_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_of_squares_variance_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_of_squares_variance_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_variance_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_variance_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_variance_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_Tubulin_haralick_sum_variance_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_angular_second_moment_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_angular_second_moment_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_angular_second_moment_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_angular_second_moment_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_contrast_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_contrast_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_contrast_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_contrast_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_correlation_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_correlation_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_correlation_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_correlation_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_difference_entropy_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_difference_entropy_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_difference_entropy_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_difference_entropy_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_difference_variance_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_difference_variance_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_difference_variance_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_difference_variance_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_entropy_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_entropy_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_entropy_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_entropy_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_information_measure_of_correlation_1_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_information_measure_of_correlation_1_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_information_measure_of_correlation_1_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_information_measure_of_correlation_1_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_information_measure_of_correlation_2_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_information_measure_of_correlation_2_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_information_measure_of_correlation_2_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_information_measure_of_correlation_2_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_inverse_difference_moment_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_inverse_difference_moment_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_inverse_difference_moment_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_inverse_difference_moment_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_average_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_average_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_average_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_average_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_entropy_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_entropy_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_entropy_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_entropy_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_of_squares_variance_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_of_squares_variance_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_of_squares_variance_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_of_squares_variance_8_270
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_variance_8_000
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_variance_8_090
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_variance_8_180
## INFO [2018-02-05 14:39:04]    Nuclei_DAPI_haralick_sum_variance_8_270

variables <-
  colnames(profiles) %>%
  str_subset("^Nuclei_|^Cells_|^Cytoplasm_")

Remove features that have near-zero variance. This dataset doesn’t have any such features, so nothing is removed.

profiles <-
  cytominer::variable_select(
    population = profiles,
    variables = variables,
    sample = profiles,
    operation = "variance_threshold"
  ) %>%
  collect()

## INFO [2018-02-05 14:39:15] excluded:
## INFO [2018-02-05 14:39:15]    Cells_Actin_euler_number
## INFO [2018-02-05 14:39:15]    Cells_Actin_moments_zernike_8_8_00
## INFO [2018-02-05 14:39:15]    Cells_Tubulin_euler_number
## INFO [2018-02-05 14:39:15]    Cells_Tubulin_moments_zernike_8_8_00
## INFO [2018-02-05 14:39:15]    Cells_DAPI_euler_number
## INFO [2018-02-05 14:39:15]    Cells_DAPI_moments_zernike_8_8_00
## INFO [2018-02-05 14:39:15]    Nuclei_Actin_euler_number
## INFO [2018-02-05 14:39:15]    Nuclei_Actin_moments_zernike_8_8_00
## INFO [2018-02-05 14:39:15]    Nuclei_Tubulin_euler_number
## INFO [2018-02-05 14:39:15]    Nuclei_Tubulin_moments_zernike_8_8_00
## INFO [2018-02-05 14:39:15]    Nuclei_DAPI_euler_number
## INFO [2018-02-05 14:39:15]    Nuclei_DAPI_moments_zernike_8_8_00

variables <-
  colnames(profiles) %>%
  str_subset("^Nuclei_|^Cells_|^Cytoplasm_")

Remove features that have poor correlation across replicates. To do so, lets first compute the correlations.

doParallel::registerDoParallel(cores = 4)

feature_replicate_correlations <-
  profiles %>%
  cytominer::variable_importance(
    variables = variables,
    strata = c("Image_Metadata_Compound", "Image_Metadata_Concentration"),
    replicates = 3,
    cores = 4)

feature_replicate_correlations %>% 
  readr::write_csv("feature_replicate_correlations.csv")

What the does the distribution look like?

ggplot(feature_replicate_correlations, aes(median))  +
  stat_ecdf() +
  geom_vline(xintercept = 0.5, color = "red") +
  xlab("median replicate correlation (Pearson)") +
  ylab("F(x)")

Here, we select a threshold and remove features that have a replicate correlation lower than that threshold

profiles %<>%
  select_(.dots = setdiff(x = colnames(profiles),
                          y = feature_replicate_correlations %>%
                            filter(median < 0.5) %>%
                            magrittr::extract2("variable"))
          )

variables <-
  colnames(profiles) %>%
  str_subset("^Nuclei_|^Cells_|^Cytoplasm_")

Filter based on correlation between features. The morphological features extracted contain several highly correlated groups. We want to to prune the set of features, retaining only one feature from each of these highly correlated sets. The function correlation_threshold provides an approximate (greedy) solution to this problem. After excluding the features, no pair of features have a correlation greater than cutoff indicated below.

profiles <-
  cytominer::variable_select(
    population = profiles,
    variables = variables,
    sample = profiles,
    operation = "correlation_threshold",
    cutoff = 0.95) %>%
  collect()

## INFO [2018-02-05 14:41:09] excluded:
## INFO [2018-02-05 14:41:09]    Cells_Actin_convex_hull_area
## INFO [2018-02-05 14:41:09]    Cells_Actin_equivalent_diameter
## INFO [2018-02-05 14:41:09]    Cells_Actin_inertia_tensor_0_0
## INFO [2018-02-05 14:41:09]    Cells_Actin_inertia_tensor_1_1
## INFO [2018-02-05 14:41:09]    Cells_Actin_inertia_tensor_eigen_values_0
## INFO [2018-02-05 14:41:09]    Cells_Actin_inertia_tensor_eigen_values_1
## INFO [2018-02-05 14:41:09]    Cells_Actin_intensity_mean
## INFO [2018-02-05 14:41:09]    Cells_Actin_intensity_quartile_3
## INFO [2018-02-05 14:41:09]    Cells_Actin_intensity_standard_deviation
## INFO [2018-02-05 14:41:09]    Cells_Actin_local_binary_patterns_01_08_06
## INFO [2018-02-05 14:41:09]    Cells_Actin_local_binary_patterns_02_08_06
## INFO [2018-02-05 14:41:09]    Cells_Actin_local_binary_patterns_06_08_06
## INFO [2018-02-05 14:41:09]    Cells_Actin_local_binary_patterns_07_08_06
## INFO [2018-02-05 14:41:09]    Cells_Actin_local_binary_patterns_08_08_06
## INFO [2018-02-05 14:41:09]    Cells_Actin_local_binary_patterns_10_08_06
## INFO [2018-02-05 14:41:09]    Cells_Actin_local_binary_patterns_11_08_06
## INFO [2018-02-05 14:41:09]    Cells_Actin_local_binary_patterns_12_08_06
## INFO [2018-02-05 14:41:09]    Cells_Actin_local_binary_patterns_13_08_06
## INFO [2018-02-05 14:41:09]    Cells_Actin_major_axis_length
## INFO [2018-02-05 14:41:09]    Cells_Actin_minor_axis_length
## INFO [2018-02-05 14:41:09]    Cells_Actin_moments_central_0_0
## INFO [2018-02-05 14:41:09]    Cells_Actin_moments_spatial_0_0
## INFO [2018-02-05 14:41:09]    Cells_Actin_moments_spatial_1_0
## INFO [2018-02-05 14:41:09]    Cells_Actin_moments_weighted_spatial_1_0
## INFO [2018-02-05 14:41:09]    Cells_Actin_solidity
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_area
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_bounding_box_area
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_centroid_weighted_local_column
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_centroid_weighted_local_row
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_convex_hull_area
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_equivalent_diameter
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_inertia_tensor_0_0
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_inertia_tensor_1_1
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_inertia_tensor_eigen_values_0
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_inertia_tensor_eigen_values_1
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_intensity_median_absolute_deviation
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_intensity_standard_deviation
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_00_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_01_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_02_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_06_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_07_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_08_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_10_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_11_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_12_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_local_binary_patterns_13_08_06
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_major_axis_length
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_minor_axis_length
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_moments_central_0_0
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_moments_spatial_0_0
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_moments_spatial_1_0
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_moments_weighted_spatial_0_1
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_moments_weighted_spatial_0_2
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_moments_weighted_spatial_1_0
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_solidity
## INFO [2018-02-05 14:41:09]    Cells_Tubulin_threshold_adjacency_statistics_35
## INFO [2018-02-05 14:41:09]    Cells_DAPI_area
## INFO [2018-02-05 14:41:09]    Cells_DAPI_bounding_box_area
## INFO [2018-02-05 14:41:09]    Cells_DAPI_centroid_weighted_local_column
## INFO [2018-02-05 14:41:09]    Cells_DAPI_centroid_weighted_local_row
## INFO [2018-02-05 14:41:09]    Cells_DAPI_convex_hull_area
## INFO [2018-02-05 14:41:09]    Cells_DAPI_equivalent_diameter
## INFO [2018-02-05 14:41:09]    Cells_DAPI_inertia_tensor_0_0
## INFO [2018-02-05 14:41:09]    Cells_DAPI_inertia_tensor_1_1
## INFO [2018-02-05 14:41:09]    Cells_DAPI_inertia_tensor_eigen_values_0
## INFO [2018-02-05 14:41:09]    Cells_DAPI_inertia_tensor_eigen_values_1
## INFO [2018-02-05 14:41:09]    Cells_DAPI_intensity_standard_deviation
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_00_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_01_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_02_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_03_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_05_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_06_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_07_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_08_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_10_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_11_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_12_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_local_binary_patterns_13_08_06
## INFO [2018-02-05 14:41:09]    Cells_DAPI_major_axis_length
## INFO [2018-02-05 14:41:09]    Cells_DAPI_minor_axis_length
## INFO [2018-02-05 14:41:09]    Cells_DAPI_moments_central_0_0
## INFO [2018-02-05 14:41:09]    Cells_DAPI_moments_spatial_0_0
## INFO [2018-02-05 14:41:09]    Cells_DAPI_moments_spatial_1_0
## INFO [2018-02-05 14:41:09]    Cells_DAPI_moments_weighted_normalized_2_0
## INFO [2018-02-05 14:41:09]    Cells_DAPI_solidity
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_area
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_bounding_box_area
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_centroid_weighted_local_column
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_centroid_weighted_local_row
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_convex_hull_area
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_equivalent_diameter
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_inertia_tensor_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_inertia_tensor_1_1
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_inertia_tensor_eigen_values_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_inertia_tensor_eigen_values_1
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_intensity_integrated
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_intensity_mean
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_intensity_minimum
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_intensity_quartile_2
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_intensity_standard_deviation
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_00_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_01_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_02_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_04_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_05_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_06_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_07_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_08_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_09_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_10_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_11_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_12_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_local_binary_patterns_13_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_major_axis_length
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_minor_axis_length
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_central_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_spatial_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_spatial_1_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_weighted_central_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_weighted_central_0_2
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_weighted_spatial_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_weighted_spatial_0_1
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_weighted_spatial_1_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_zernike_8_8_07
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_zernike_8_8_12
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_zernike_8_8_13
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_zernike_8_8_17
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_zernike_8_8_18
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_zernike_8_8_21
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_zernike_8_8_22
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_moments_zernike_8_8_23
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_perimeter
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_threshold_adjacency_statistics_25
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_threshold_adjacency_statistics_26
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_threshold_adjacency_statistics_33
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_threshold_adjacency_statistics_34
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_threshold_adjacency_statistics_35
## INFO [2018-02-05 14:41:09]    Cytoplasm_Actin_threshold_adjacency_statistics_45
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_area
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_bounding_box_area
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_centroid_weighted_local_column
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_centroid_weighted_local_row
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_convex_hull_area
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_equivalent_diameter
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_extent
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_inertia_tensor_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_inertia_tensor_1_1
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_inertia_tensor_eigen_values_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_inertia_tensor_eigen_values_1
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_intensity_integrated
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_intensity_maximum
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_intensity_minimum
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_intensity_quartile_2
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_intensity_quartile_3
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_intensity_standard_deviation
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_00_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_01_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_02_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_04_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_05_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_06_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_07_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_08_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_09_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_10_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_11_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_12_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_local_binary_patterns_13_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_major_axis_length
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_minor_axis_length
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_central_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_hu_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_normalized_0_2
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_spatial_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_spatial_1_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_weighted_central_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_weighted_central_0_2
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_weighted_spatial_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_weighted_spatial_0_1
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_weighted_spatial_0_2
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_weighted_spatial_1_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_09
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_10
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_12
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_13
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_16
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_17
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_18
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_20
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_21
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_22
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_moments_zernike_8_8_23
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_perimeter
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_threshold_adjacency_statistics_25
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_threshold_adjacency_statistics_26
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_threshold_adjacency_statistics_35
## INFO [2018-02-05 14:41:09]    Cytoplasm_Tubulin_threshold_adjacency_statistics_45
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_area
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_bounding_box_area
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_centroid_weighted_local_column
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_centroid_weighted_local_row
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_convex_hull_area
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_equivalent_diameter
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_extent
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_inertia_tensor_0_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_inertia_tensor_1_1
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_inertia_tensor_eigen_values_0
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_inertia_tensor_eigen_values_1
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_intensity_standard_deviation
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_00_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_01_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_02_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_03_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_04_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_05_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_06_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_07_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_08_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_09_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_10_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_11_08_06
## INFO [2018-02-05 14:41:09]    Cytoplasm_DAPI_local_binary_patterns_12_08_06
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_local_binary_patterns_13_08_06
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_major_axis_length
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_minor_axis_length
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_central_0_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_hu_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_normalized_0_2
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_spatial_0_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_spatial_1_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_weighted_normalized_0_2
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_weighted_spatial_0_1
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_09
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_10
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_12
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_13
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_17
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_18
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_21
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_22
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_23
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_perimeter
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_03
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_04
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_05
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_09
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_10
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_14
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_15
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_16
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_17
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_18
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_19
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_25
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_26
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_27
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_28
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_29
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_30
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_35
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_45
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_52
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_centroid_weighted_local_column
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_convex_hull_area
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_inertia_tensor_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_inertia_tensor_1_1
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_inertia_tensor_eigen_values_1
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_intensity_maximum
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_intensity_mean
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_intensity_median
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_intensity_quartile_2
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_intensity_quartile_3
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_intensity_standard_deviation
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_local_binary_patterns_01_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_local_binary_patterns_06_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_local_binary_patterns_07_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_local_binary_patterns_10_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_local_binary_patterns_11_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_local_binary_patterns_12_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_local_binary_patterns_13_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_central_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_spatial_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_spatial_0_1
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_spatial_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_spatial_1_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_spatial_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_spatial_0_1
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_spatial_1_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_spatial_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_perimeter
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_02
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_11
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_19
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_32
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_33
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_35
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_38
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_45
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_53
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_area
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_bounding_box_area
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_centroid_weighted_local_column
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_centroid_weighted_local_row
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_convex_hull_area
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_equivalent_diameter
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_inertia_tensor_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_inertia_tensor_1_1
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_inertia_tensor_eigen_values_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_inertia_tensor_eigen_values_1
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_intensity_integrated
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_intensity_maximum
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_intensity_mean
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_intensity_median
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_intensity_minimum
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_intensity_quartile_2
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_intensity_quartile_3
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_intensity_standard_deviation
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_local_binary_patterns_01_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_local_binary_patterns_04_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_local_binary_patterns_06_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_local_binary_patterns_07_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_local_binary_patterns_10_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_local_binary_patterns_11_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_local_binary_patterns_12_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_local_binary_patterns_13_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_major_axis_length
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_central_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_central_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_central_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_spatial_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_spatial_0_1
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_spatial_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_spatial_1_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_spatial_1_1
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_spatial_1_2
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_spatial_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_central_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_central_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_spatial_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_spatial_0_1
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_spatial_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_spatial_1_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_spatial_1_1
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_spatial_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_zernike_8_8_05
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_perimeter
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_11
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_18
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_19
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_20
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_22
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_33
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_35
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_36
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_45
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_49
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_area
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_bounding_box_area
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_centroid_weighted_local_column
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_centroid_weighted_local_row
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_convex_hull_area
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_equivalent_diameter
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_inertia_tensor_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_inertia_tensor_1_1
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_inertia_tensor_eigen_values_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_inertia_tensor_eigen_values_1
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_intensity_maximum
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_intensity_median_absolute_deviation
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_intensity_quartile_3
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_intensity_standard_deviation
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_local_binary_patterns_04_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_local_binary_patterns_06_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_local_binary_patterns_07_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_local_binary_patterns_09_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_local_binary_patterns_10_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_local_binary_patterns_13_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_major_axis_length
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_central_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_central_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_central_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_spatial_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_spatial_0_1
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_spatial_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_spatial_1_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_spatial_1_1
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_spatial_1_2
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_spatial_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_weighted_spatial_0_1
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_weighted_spatial_1_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_weighted_spatial_1_1
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_weighted_spatial_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_perimeter
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_threshold_adjacency_statistics_02
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_threshold_adjacency_statistics_24
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_threshold_adjacency_statistics_26
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_threshold_adjacency_statistics_32
## INFO [2018-02-05 14:41:10]    Cells_Actin_area
## INFO [2018-02-05 14:41:10]    Cells_Actin_bounding_box_area
## INFO [2018-02-05 14:41:10]    Cells_Actin_centroid_weighted_local_column
## INFO [2018-02-05 14:41:10]    Cells_Actin_intensity_median
## INFO [2018-02-05 14:41:10]    Cells_Actin_local_binary_patterns_03_08_06
## INFO [2018-02-05 14:41:10]    Cells_Actin_intensity_integrated
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_weighted_central_0_0
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_weighted_central_0_2
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_weighted_spatial_0_2
## INFO [2018-02-05 14:41:10]    Cells_Actin_centroid_weighted_local_row
## INFO [2018-02-05 14:41:10]    Cells_Actin_local_binary_patterns_00_08_06
## INFO [2018-02-05 14:41:10]    Cells_Actin_shannon_entropy_hartley
## INFO [2018-02-05 14:41:10]    Cells_Actin_shannon_entropy_natural
## INFO [2018-02-05 14:41:10]    Cells_Actin_threshold_adjacency_statistics_33
## INFO [2018-02-05 14:41:10]    Cells_Actin_threshold_adjacency_statistics_37
## INFO [2018-02-05 14:41:10]    Cells_Actin_eccentricity
## INFO [2018-02-05 14:41:10]    Cells_Actin_extent
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_intensity_maximum
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_intensity_median
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_intensity_mean
## INFO [2018-02-05 14:41:10]    Cells_Actin_local_binary_patterns_04_08_06
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_local_binary_patterns_03_08_06
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_hu_0
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_hu_2
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_normalized_0_2
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_normalized_2_2
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_spatial_0_1
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_spatial_1_1
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_spatial_2_0
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_intensity_integrated
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_weighted_central_0_0
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_weighted_central_0_2
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_zernike_8_8_04
## INFO [2018-02-05 14:41:10]    Cells_Actin_perimeter
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_shannon_entropy_hartley
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_shannon_entropy_natural
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_threshold_adjacency_statistics_37
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_eccentricity
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_extent
## INFO [2018-02-05 14:41:10]    Cells_DAPI_intensity_median
## INFO [2018-02-05 14:41:10]    Cells_DAPI_intensity_mean
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_hu_0
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_hu_2
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_normalized_0_2
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_normalized_2_2
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_spatial_0_1
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_spatial_1_1
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_spatial_2_0
## INFO [2018-02-05 14:41:10]    Cells_DAPI_intensity_integrated
## INFO [2018-02-05 14:41:10]    Cells_DAPI_moments_hu_weighted_0
## INFO [2018-02-05 14:41:10]    Cells_DAPI_moments_weighted_central_0_0
## INFO [2018-02-05 14:41:10]    Cells_DAPI_moments_weighted_spatial_0_1
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_perimeter
## INFO [2018-02-05 14:41:10]    Cells_DAPI_shannon_entropy_hartley
## INFO [2018-02-05 14:41:10]    Cells_DAPI_shannon_entropy_natural
## INFO [2018-02-05 14:41:10]    Cells_DAPI_threshold_adjacency_statistics_33
## INFO [2018-02-05 14:41:10]    Cells_Actin_intensity_maximum
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_intensity_median
## INFO [2018-02-05 14:41:10]    Cells_Actin_intensity_median_absolute_deviation
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_hu_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_normalized_0_2
## INFO [2018-02-05 14:41:10]    Cells_DAPI_moments_spatial_0_1
## INFO [2018-02-05 14:41:10]    Cells_DAPI_moments_spatial_2_0
## INFO [2018-02-05 14:41:10]    Cells_Actin_moments_weighted_spatial_1_1
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_weighted_spatial_0_2
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_03
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_04
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_05
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_09
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_08
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_06
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_10
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_11
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_14
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_16
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_15
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_zernike_8_8_19
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_shannon_entropy_hartley
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_shannon_entropy_natural
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_extent
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_threshold_adjacency_statistics_17
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_threshold_adjacency_statistics_36
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_eccentricity
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_intensity_quartile_3
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_intensity_median
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_local_binary_patterns_03_08_06
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_local_binary_patterns_04_08_06
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_normalized_2_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_spatial_0_1
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_moments_spatial_2_0
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_weighted_spatial_1_1
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_03
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_04
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_06
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_05
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_07
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_08
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_11
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_14
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_15
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_zernike_8_8_19
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_shannon_entropy_hartley
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_shannon_entropy_natural
## INFO [2018-02-05 14:41:10]    Cytoplasm_Actin_solidity
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_threshold_adjacency_statistics_32
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_threshold_adjacency_statistics_33
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_threshold_adjacency_statistics_34
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_threshold_adjacency_statistics_36
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_threshold_adjacency_statistics_37
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_eccentricity
## INFO [2018-02-05 14:41:10]    Cells_DAPI_intensity_minimum
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_intensity_median
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_normalized_2_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_spatial_0_1
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_moments_spatial_2_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_intensity_integrated
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_hu_weighted_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_weighted_central_0_0
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_03
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_04
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_06
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_05
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_07
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_08
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_11
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_14
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_16
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_15
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_20
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_moments_zernike_8_8_19
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_shannon_entropy_hartley
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_shannon_entropy_natural
## INFO [2018-02-05 14:41:10]    Cytoplasm_Tubulin_solidity
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_00
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_06
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_07
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_02
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_13
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_threshold_adjacency_statistics_31
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_area
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_centroid_weighted_local_row
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_bounding_box_area
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_intensity_median_absolute_deviation
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_inertia_tensor_eigen_values_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_local_binary_patterns_02_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_equivalent_diameter
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_central_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_central_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_spatial_1_1
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_spatial_1_2
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_intensity_integrated
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_central_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_central_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_central_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_spatial_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_spatial_1_1
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_spatial_1_2
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_weighted_spatial_2_1
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_shannon_entropy_hartley
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_shannon_entropy_natural
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_10
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_09
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_18
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_25
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_20
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_threshold_adjacency_statistics_37
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_eccentricity
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_local_binary_patterns_00_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_major_axis_length
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_minor_axis_length
## INFO [2018-02-05 14:41:10]    Nuclei_Actin_moments_spatial_2_1
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_central_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_spatial_1_2
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_weighted_spatial_2_1
## INFO [2018-02-05 14:41:10]    Cells_Tubulin_moments_zernike_8_8_05
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_shannon_entropy_hartley
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_shannon_entropy_natural
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_10
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_09
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_12
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_13
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_24
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_25
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_threshold_adjacency_statistics_21
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_eccentricity
## INFO [2018-02-05 14:41:10]    Cells_DAPI_intensity_maximum
## INFO [2018-02-05 14:41:10]    Cytoplasm_DAPI_intensity_maximum
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_intensity_median
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_local_binary_patterns_01_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_local_binary_patterns_08_08_06
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_minor_axis_length
## INFO [2018-02-05 14:41:10]    Nuclei_Tubulin_moments_spatial_2_1
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_intensity_integrated
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_weighted_central_0_2
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_weighted_central_0_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_moments_weighted_central_2_0
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_shannon_entropy_hartley
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_shannon_entropy_natural
## INFO [2018-02-05 14:41:10]    Nuclei_DAPI_threshold_adjacency_statistics_33

variables <-
  colnames(profiles) %>%
  str_subset("^Nuclei_|^Cells_|^Cytoplasm_")

Normalize with reference to DMSO

There may be plate-to-plate variations, which can be compensated for to some extent by normalizing the features with respect to the DMSO wells per plate.

profiles <-
  cytominer::normalize(
    population = profiles,
    variables = variables,
    strata =  c("Image_Metadata_Plate"),
    sample = profiles %>% filter(Image_Metadata_Compound == "DMSO")
  )

profiles <-
  cytominer::variable_select(
      population = profiles,
      variables = variables,
      operation = "drop_na_columns"
  )

variables <-
  colnames(profiles) %>%
  str_subset("^Nuclei_|^Cells_|^Cytoplasm_")

Calculate treatment profiles and predict mechanism-of-action

We have selected features and normalized the data. We can now compute treatment profiles by averaging across replicates.

profiles <-
  cytominer::aggregate(
    population = profiles,
    variables = variables,
    strata = c("Image_Metadata_Compound",
               "Image_Metadata_Concentration",
               "Image_Metadata_MoA"),
    operation = "mean"
  )

variables <-
  colnames(profiles) %>%
  str_subset("^Nuclei_|^Cells_|^Cytoplasm_")

Let’s visualize this data using t-SNE.

profiles %<>%
  filter(Image_Metadata_Compound != "DMSO")

correlation <-
  profiles %>%
  select(one_of(variables)) %>%
  as.matrix() %>%
  t() %>%
  cor()

mechanism <- as.character(profiles$Image_Metadata_MoA)

set.seed(123)

df <-
  tibble::as_data_frame(
    tsne::tsne(as.dist(1-correlation))
    ) %>%
  mutate(mechanism = mechanism)

p <-
  ggplot(df, aes(V1, V2, color=mechanism)) +
  geom_point() +
  ggtitle("t-SNE visualization of compound profiles")

print(p)

The data clusters into mechanisms quite nicely. Let’s quantify this by evaluating how well we can predict mechanism-of-action by simply assigning a treatment the mechanism of its nearest neighbor. NOTE: A common mistake when analyzing this dataset is to not exclude other concentrations of the same compound when looking up the nearest neighbor. That is cheating! mask in the code below addresses this.

compound <- profiles$Image_Metadata_Compound

mask <- as.integer(outer(compound, compound, FUN="!="))

mask[mask == 0] <- -Inf

correlation_masked <- correlation * mask

prediction <- sapply(1:nrow(correlation_masked),
               function(i) mechanism[order(correlation_masked[i,],
                                           decreasing = TRUE)[1]])

confusion_matrix <- caret::confusionMatrix(prediction, mechanism)

What’s the classification accuracy?

tibble::frame_data(
  ~metric, ~value,
  "Accuracy", sprintf("%.2f", confusion_matrix$overall["Accuracy"]),
  "95% CI", sprintf("(%.2f, %.2f)", confusion_matrix$overall[["AccuracyLower"]],
                    confusion_matrix$overall[["AccuracyUpper"]])
  ) %>%
  knitr::kable(digits = 2)

metric	value
Accuracy	0.75
95% CI	(0.65, 0.83)

What does the whole confusion matrix look like?

confusion_matrix$table %>%
  knitr::kable()

	Actin disruptors	Aurora kinase inhibitors	Cholesterol-lowering	DNA damage	DNA replication	Eg5 inhibitors	Epithelial	Kinase inhibitors	Microtubule destabilizers	Microtubule stabilizers	Protein degradation	Protein synthesis
Actin disruptors	3	0	0	0	0	0	0	0	0	0	0	0
Aurora kinase inhibitors	0	8	0	0	0	0	0	0	0	1	0	0
Cholesterol-lowering	0	0	6	0	0	0	0	0	0	0	0	0
DNA damage	0	4	0	9	3	0	0	0	0	0	0	0
DNA replication	0	0	0	0	3	0	0	0	0	0	1	0
Eg5 inhibitors	0	0	0	0	1	8	2	0	1	1	0	0
Epithelial	0	0	0	0	0	1	4	0	0	0	0	0
Kinase inhibitors	0	0	0	0	0	0	0	5	0	0	0	0
Microtubule destabilizers	0	0	0	0	0	2	0	0	13	0	0	0
Microtubule stabilizers	2	0	0	0	0	1	0	0	0	6	1	0
Protein degradation	0	0	0	0	1	0	0	0	0	1	4	0
Protein synthesis	0	0	0	0	0	0	2	0	0	0	1	8

Predict compounds mechanism-of-action by morphological profiling

Allen Goodman and Shantanu Singh

2018-02-05

Load data

Feature selection

Normalize with reference to DMSO

Calculate treatment profiles and predict mechanism-of-action