Fouga / BaSiC

A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images

BaSiC

This is a fork of the BaSiC backgound correction pipeline. To run the pipeline for 2 photon microscopy Tissue Vision data, you need to clone this repository and StitchIt.

Example

source_dir = '/DATA_NAME/'; % here you need to have rawData directory with all your data and a Mosaic.txt

addpath(genpath('FULL_PATH/StitchIt/code/')); % add path to the StitchIt(https://github.com/BaselLaserMouse/StitchIt).

addpath(genpath('FULL_PATH/BaSiC/')); % add path to the BaSiC (https://github.com/Fouga/BaSiC) 

cd (source_dir);

% maKE INI FILE
if ~exist('stitchitConf.ini')
	makeLocalStitchItConf
end

% read info from Mosaic.txt 
M=readMetaData2Stitchit;

%check for and fix missing tiles if this was a TissueCyte acquisition
if strcmp(M.System.type,'TissueCyte')
    writeBlacktile = 0;
    missingTiles=identifyMissingTilesInDir('rawData',0,0,[],writeBlacktile);
else
    missingTiles = -1;
end

% correct background illumination with cidre
alternativeIlluminationCorrection('basic')


% stitch all the data
stitchAllChannels

A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images

by Tingying Peng, Kurt Thorn, Timm Schroeder, Lichao Wang, Fabian J Theis, Carsten Marr*, Nassir Navab*, Nature Communication 8:14836 (2017). doi: 10.1038/ncomms14836.

BaSiC is licensed under

Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Public License

It is free for academic use and please contact us for any commercial use.

Demo

Download demo data examples from Dropbox and run matlab files under example folder.

ImageJ/Fiji Plugin

BaSiC is also available as a ImageJ/Fiji Plugin. Plugin and installation instruction can be found in BaSiC Software Website.

Acknowledgements

• Rob Campbell for Stichit algorithm.
• Tingying Peng for BaSiC.
• And Gus Brown for recurcive directory listing rdir.