Explore the Single-Cell Cartography tools featured in CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia within this repository.
Documentation about CartoCell pipeline can be found clicking here.

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Main features extraction

codes inside: NaturalVariation/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.

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Some interesting user interfaces (_ui) for spatial distribution study:

Inside NaturalVariation/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

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Semiautomatic curation | proofreading tools

Some interesting tools can be found inside NaturalVariation/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.