Published August 16, 2023 | Version v1
Software Open

Code and example dataset associated with "Enhanced cell viscosity: a new phenotype associated with lamin A/C alterations"

Description

README

Date: 16/08/23

Code associated with manuscript: Enhanced cell viscosity as a marker of premature senescence induced by lamin A/C alterations

Codes by Cécile JEBANE

Upload by Jean-Francois RUPPRECHT

 

Main code (MATLAB R2023a): Length_seg.m to analyze segmented cell films.

Code to analyze the curves (MATLAB R2023a) (produced by Length_seg.m): curve.m and curve.fig (the "save" button, "get nucleus" and the "smooth curve" slider don't currently work), it's used to open the "in_out_summary.mat" file (the other files not mentioned are used here (selectdata,subfolder etc), beware it only works with cells, it won't work on nuclei, if you need to add the code that works for nuclei tell me I'll add it). The "channel test" folder contains the sample films of the cells already analyzed.

Code for segmenting the cell in the channel (MATLAB R2023a): Segment_Cells.ijm (you can test with the images in the "channel test" folder).

Code to analyze nuclei in fluorescence (MATLAB R2023a): Track_nuclei.m & region_seg.m, it works with a GPU. 

Code to extract the cell volume (FIJI): volumeConfocal.ijm  To be used on the data within the "cells confocal" folder, an original example film & the segmented one. The code works on the segmented one.

Files

Jebane_Rc_Lt.zip

Files (287.4 MB)

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