Single cell cartography tools for CartoCell
Collection of all the codes needed for the single cell cartography study using segmentations from the CartoCell pipeline.
Feature extraction
Run mainFeaturesExtraction_20xCysts.m for extracting cyst features. Result will be writen in a xls table.
codes inside:
NaturalVariation-CartoCell_SingleCellCartographyTools_1.0.0/Code/src/lib/featuresExtraction_20x/
mainFeaturesExtraction_20xCysts
Code for extracting cyst features.
Result will be writen in a xls table.
Running the code will display some User Interface so no coding is needed to extract features.
Global Features | Polygon Distributions | Mean Cell Features | Std Cell Features
mainCellFeaturesExtraction_20xCysts
Code for extracting cyst Cell Features.
Result will be writen in a xls table.
Variables are the same as mainFeaturesExtraction_20xCysts/meanCellFeatures but raw
instead of averaged.
Running the code will display some User Interface so no coding is needed to extract features.
Single cell cartography tools
To join cell's variable info with cell's Z and XY Position run getCellSpatialData_ui.m
For 3D renderings with cell features information color-coded run plotSpatialDistribution_ui.m
For plotting scatter plots and histogram plots with cell features information color-coded run plotGradientBoomerangs.m
Inside NaturalVariation-CartoCell_SingleCellCartographyTools_1.0.0/Code/src/lib/cartography/
getCellSpatialData_ui
Function that joins cell's variable info with cell's Z and XY Position
getCellSpatialStatisticsBULKplot_ui [RETURNS TABLE AND TABLE FOR PLOTVIOLIN]
For each Variable Quartile, calculates mean ZPos of cells in that Quartile.
If scutoids just the mean of ZPos (no quartiles)
plotSpatialDistribution_ui
Plotting 3D renders with feature information color-coded
plotSpatialDistributionBULK_ui
Plotting 3D renders with all features information color-coded
plotGradientBoomerangs
For each quartile (or rank) of selected variable's distribution
a scatter plot and histogram plot is plotted and saved
Proofreading
In case of unsatisfactory segmentations, this section is designed to correct them. Run checkingSegmentedCysts.m to extract in a table the possible segmentation errors. Run saveForValidation.m to prepare the images for the proofreading process. Finally, run bulkCystProofreading.m to launch the proofreading GUI (Graphic User Interface).
Some interesting tools can be found inside NaturalVariation-CartoCell_SingleCellCartographyTools_1.0.0/Code/src/lib/proofreading/
checkingSegmentedCysts
Code for creating the warning table used by bulkCystProofReading.
This table contains info of potentially misslabeled cells.
saveForValidation
Code for creating the mat files needed for bulkCystProofreading tool
bulkCystProofreading
Main code for semiautomatic curation GUI.
