Name:
Quantification of protein expression in dark patches

Version:
2

Type:
Script/Macro

Keywords:
ImageJ,Quantification,Fiji,macro

Requirements:
Requires Fiji

Brief Description:
Quantification of Cy5  protein expression in dark patches.

Detailed Explanation:
Quantify channel2 expression inside dark patches found in channel1.
1. Open macro file in Fiji and click Run
2. Input must be a folder with images (or with folders with images inside) that are either .png or .tif files
3. Choose input folder and output folder (main folder containing results) after running the macro
4. Output is a folder with the same name as input image with the following content: zip file with ROIs of dark patches; Csv file with the measurements of each ROI in channel2; and the input image in the composite format. 
Csv files can be used in Excel for posterior data analysis. Any editable parameters require changing the code itself. Hopefully, each parameter is easy to find by reading the comments existent throughout the macro.


DataSet Description:
Maximum intensity projected Confocal images of a drosophila imaginal disc, acquired using Leica SP5 and a 40x objective. Staining is ubi-GFP (channel 1) , Cy3 (channel3) and Cy5 (channel2).

External Location:
https://github.com/zeserrado-marques/Quantification-of-protein-expression-inside-dark-patches/blob/master/Quantificationproteinexpressiondarkpatches_v1.2.ijm

Link To Publication:


Authors:
José Serrado Marques - IGC - Instituto Gulbenkian de Ciência