Results

Results Folder

The results folder is organized into several subfolders to store different types of output data from the HiTIPS analysis:

• configuration_files: Includes the ‘analysis_configuration’ file that were used or generated during the analysis, ‘dependencies_versions’ that includes all the packages and their versions used for the analysis, and ‘erros_log’ that logs the errors (if any) during the analysis.

• nuclei_masks: Holds the generated masks for the segmented cell nuclei, crucial for identifying and analyzing individual cells and nuclei tracking.

• well_nuclei_results: Results related to the nuclei that have been analyzed and saved separately for each well of the plate.

• well_spots_locations: Contains information about the locations of spots detected and saved separately for each well of the plate.

• whole_plate_results: Stores comprehensive results that pertain to the entire plate rather than individual wells or nuclei.

• cell_tracking: Contains files related to the tracking of nuclei and spots across different time points. This folder contais the followinng subfolders:

  • ‘annotated_spot_image_patches’: Contains time-stacks of the nuclei with detected spots. Spots are tracked over time and annotated by spot label.

  • ‘single_track_images’: This folder includes time-stacks of the each tracked nuclei before and after frame to frame registration.

  • ‘single_track_tables’: Contains information related to each tracked nucleous over time. Each file is for a separate nucleus.

  • ‘spot_image_patches’: Contains time-stacks of the nuclei with detected spots. Spots are tracked over time and but are not annotated.

  • ‘spot_intensity_tables’: This contais both csv and txt file for each spot that stores the location, intensity and HMM information related to the spots.

  -‘whole_field_track_images’: This folder contains tracked and annotated nuclei within each field over time.

Table of information for the segmented cell nuclei

The table below describes the individual columns in that contain all the extracted information from the cell nuceli using HiTIPS.

Column Descriptions for Nuclei_Information.csv

Column Name	Description
Experiment	Identifier for the experiment or study.
column	The column location of the cell nucleus.
row	The row location of the cell nucleus.
time_point	The time point at which the data was recorded.
field_index	Index indicating the field or view within the well.
z_slice	The slice or depth at which the image is taken.
action_index	Index representing a specific action or event.
cell_index	Index for identifying individual cells.
centroid-0	The X-coordinate of the nucleus centroid.
centroid-1	The Y-coordinate of the nucleus centroid.
orientation	Orientation of the nucleus, in radians.
major_axis_length	Length of the major axis of the nucleus.
minor_axis_length	Length of the minor axis of the nucleus.
area	Area of the nucleus.
max_intensity	Maximum intensity value within the nucleus.
min_intensity	Minimum intensity value within the nucleus.
mean_intensity	Mean intensity value within the nucleus.
perimeter	Perimeter or boundary length of the nucleus.
solidity	Measure of how solid or filled the nucleus is.
sum_intensity	Sum of intensity values within the nucleus.
efc_ratio	Ratio of eccentricity of the nucleus.

Table of information for the detected spots

The table below describes the individual columns that contain all the extracted information from the spots using HiTIPS.

Column Descriptions for Spots_Information.csv

Column Name	Description
Experiment	Identifier for the experiment or study.
column	The column location of the spot.
row	The row location of the spot.
time_point	The time point at which the data was recorded.
field_index	Index indicating the field or view in the study.
z_slice	The slice or depth at which the image is taken.
channel	The channel or color of the spot.
action_index	Index representing a specific action or event.
cell_index	Index for identifying individual cells.
x_location	The X-coordinate of the spot.
y_location	The Y-coordinate of the spot.
z_location	The Z-coordinate of the spot.
radial_distance	Radial distance of the spot.
area	Area of the spot.
max_intensity	Maximum intensity value within the spot.
min_intensity	Minimum intensity value within the spot.
mean_intensity	Mean intensity value within the spot.
perimeter	Perimeter or boundary length of the spot.
solidity	Measure of how solid or filled the spot is.
bbox-0	Bounding box coordinate 0 of the spot.
bbox-1	Bounding box coordinate 1 of the spot.
bbox-2	Bounding box coordinate 2 of the spot.
bbox-3	Bounding box coordinate 3 of the spot.
center_of_mass_coords	Coordinates of the spot’s center of mass.
max_intensity_coords	Coordinates of the maximum intensity within the spot.
integrated_intensity	Integrated intensity value within the spot.
spot_area_mean	Mean area of spots.
spot_area_std	Standard deviation of spot areas.
spot_area_median	Median area of spots.
spot_max_to_min	Maximum to minimum intensity ratio within the spot.
spot_to_area_mean	Mean ratio of spot intensity to area.
spot_max_to_area_mean	Mean ratio of maximum intensity to area within spots.

Cell Tracking Tables

Column Descriptions for Nuclei_Tracking_Information.csv

Column Name	Description
ID	Identifier for the nucleus.
t	Time point of nucleus tracking.
x	X-coordinate of the nucleus.
y	Y-coordinate of the nucleus.
z	Z-coordinate of the nucleus.
parent	Identifier of the parent nucleus.
root	Identifier of the root nucleus.
state	State of the nucleus.
generation	Generation level of the nucleus.
eccentricity	Eccentricity of the nucleus.
bbox-0	Bounding box beginning X coordinate of the nucleus.
bbox-1	Bounding box end X coordinate of the nucleus.
bbox-2	Bounding box beginning Y coordinate of the nucleus.
bbox-3	Bounding box end Y coordinate of the nucleus.
solidity	Measure of how solid or filled the nucleus is.
orientation	Orientation of the nucleus.
perimeter	Perimeter or boundary length of the nucleus.
area	Area of the nucleus.
major_axis_length	Length of the major axis of the nucleus.
chXXX_spots_number	Number of spots in channel XXX associated with the nucleus.
chXXX_spots_locations	Locations of spots in channel XXX associated with the nucleus.
chXXX_patch_spots_locations	Patched locations of spots in channel XXX.
chXXX_transformed_spots_locations	Transformed locations of spots in channel XXX.
chXXX_integrated_intensity	Integrated intensity in channel XXX.
chXXX_spot_no_YYY_locations	Locations of spot no. YYY in channel XXX.
chXXX_spot_no_YYY_integrated_intensity	Integrated intensity of spot no. YYY in channel XXX.
chXXX_spot_no_YYY_x	X-coordinate of spot no. YYY in channel XXX.
chXXX_spot_no_YYY_y	Y-coordinate of spot no. YYY in channel XXX.
column	Well column location of the nucleus inside the plate.
row	Well row location of the nucleus inside the plate.
field_index	Field or view in the well.
channel	Channel or image the image containing the spot.
chXXX_spot_no_YYY_HMM_state	Hidden Markov Model (HMM) state of spot no. YYY in channel XXX.

Spot Tracking Tables

Column Descriptions for Spot_Intensity_Information.csv

Column Name	Description
column	Well column location of the spot inside the plate.
row	Well row location of the spot inside the plate.
field_index	Field or view in the well.
channel	Channel or image containing the spot.
t	Time point of spot tracking.
chXXX_spot_no_YYY_x	X-coordinate of spot no. YYY in channel XXX.
chXXX_spot_no_YYY_y	Y-coordinate of spot no. YYY in channel XXX.
chXXX_spot_no_YYY_integrated_intensity	Integrated intensity of spot no. YYY in channel XXX.