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.
codes inside: NaturalVariation/Code/src/lib/featuresExtraction_20x/
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
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.
Inside NaturalVariation/Code/src/lib/cartography/
Function that joins cell's variable info with cell's Z and XY Position
For each Variable Quartile, calculates mean ZPos of cells in that Quartile. If scutoids just the mean of ZPos (no quartiles)
Plotting 3D renders with feature information color-coded
Plotting 3D renders with all features information color-coded
For each quartile (or rank) of selected variable's distribution a scatter plot and histogram plot is plotted and saved
Some interesting tools can be found inside NaturalVariation/Code/src/lib/proofreading/
Code for creating the warning table used by bulkCystProofReading. This table contains info of potentially misslabeled cells.
Code for creating the mat files needed for bulkCystProofreading tool
Main code for semiautomatic curation GUI.
