Corsen handbook

The Corsen documentation is composed of two parts: A quick guide and a more in-depth documentation.

Analysis phases

This section describe all the steps of a Corsen analysis:

Phase name Description Tool Input file(s) Output file(s)
Data collection 3D Image acquisition. Image acquisition software (e.g. Metamorph) None Tiff, Jpeg...
Data collection Preprocessing (e.g. remove background, choose cells...). Image processing software (e.g. ImageJ) Tiff, Jpeg... Tiff, Jpeg...
3D segmentation and feature extraction Extract 3D particles from images and extract particles features. Corsen ImageJ plug-in Tiff, Jpeg... .par file
Distance analysis Compute distances between 3D particles. Corsen application .par files .data, .iv, .txt
Statistical analysis Statistical assessment of localization issue,quantification of population heterogeneity. Statistical software (e.g. R, numpy, Matlab...) .data, .iv, .txt

Files types

The following table summaries all the types of files used in a Corsen analysis:

File extension(s) Description
.tiff, .tif, .jpeg ... Image file
.par Particles file
.data Cells distance table
.iv Cells particles feature table
.txt Population table

Note that jpeg images are usually not convenient for Corsen analysis as the compression used to store data is lossly.

Sample files

We provide in this section some samples files to test Corsen.

Image files

The samples presented in this section show the localization or the non-localization of two RNAm (ATP2 and ATP16) with the mitochondria in Saccharomyces cerevisiae.

Note: Image after processing were obtained using the processing macro followed by a isodata threshold. The resulting image was used as a mask to select particles areas on the initial one.

Pars files

The following files are the output of the Corsen plug-in on the previous "after processing" images with a threshold at 1. Note that in this files the Z factor is equals to 3 (You must set this value in Corsen settings).

For specific usage, you will find next .par files with 0 or 1 particle (with only on point) :