Key
stringlengths 3
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| Value
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|---|---|
channels | [0, 1, 2, 3] |
cell_mask_dim | 4 |
cell_min_size | 8000 |
nucleus_mask_dim | 5 |
nucleus_min_size | 2000 |
pathogen_mask_dim | 6 |
pathogen_min_size | 500 |
cytoplasm_min_size | 0 |
png_size | [[224, 224]] |
png_dims | [0, 2, 3] |
include_uninfected | True |
n_job | 25 |
src | /home/carruthers/datasets/plate1/merged |
test_mode | False |
test_nr | 10 |
save_measurements | True |
radial_dist | True |
calculate_correlation | True |
manders_thresholds | [15, 85, 95] |
homogeneity | True |
homogeneity_distances | [8, 16, 32] |
save_arrays | False |
save_png | True |
use_bounding_box | False |
normalize | False |
normalize_by | png |
crop_mode | ['cell'] |
dialate_pngs | False |
dialate_png_ratios | [0.2] |
timelapse | False |
timelapse_objects | ['cell'] |
plot | False |
plot_filtration | False |
representative_images | False |
cytoplasm | True |
merge_edge_pathogen_cells | True |
experiment | exp |
metadata_type | cellvoyager |
custom_regex | null |
experiment | mitoscreen |
channels | [0, 1, 2, 3] |
nucleus_channel | 0 |
nucleus_background | 500 |
nucleus_Signal_to_noise | 4 |
nucleus_CP_prob | 0 |
remove_background_nucleus | True |
cell_channel | 1 |
cell_background | 200 |
cell_Signal_to_noise | 20 |
cell_CP_prob | -1 |
remove_background_cell | False |
pathogen_model | null |
pathogen_channel | 2 |
pathogen_background | 200 |
pathogen_Signal_to_noise | 20 |
pathogen_CP_prob | -1 |
remove_background_pathogen | True |
magnification | 40 |
save | True |
preprocess | True |
masks | True |
batch_size | 50 |
filter | False |
merge_pathogens | True |
plot | True |
adjust_cells | True |
test_mode | False |
test_images | 20 |
random_test | True |
src | /home/carruthers/datasets/plate1 |
workers | 28 |
randomize | True |
verbose | True |
nucleus_FT | 100 |
cell_FT | 100 |
pathogen_FT | 100 |
figuresize | 20 |
cmap | inferno |
normalize | True |
normalize_plots | True |
examples_to_plot | 1 |
lower_percentile | 2 |
timelapse | False |
fps | 2 |
timelapse_displacement | null |
timelapse_memory | 3 |
timelapse_frame_limits | [0, 10] |
timelapse_remove_transient | False |
timelapse_mode | trackpy |
timelapse_objects | ['cell'] |
all_to_mip | False |
pick_slice | False |
skip_mode | 1 |
upscale | False |
upscale_factor | 2 |
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