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. .. table:: 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. .. table:: 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 -------------------- .. table:: 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 -------------------- .. table:: 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. | +----------------------------------------+---------------------------------------------------------------+