Do real, customizable image processing with QuPath & ImageJ. Grab regions, apply color deconvolution, detect & measure stained pixels, send results back. Mar 7, 2018 Script of the Day: Extracting image regions to ImageJ Enter the world of ImageJ, grabbing pixels as ImagePlus objects for further processing. Once you have entered the command line and hit Enter, the desired folder location will appear on the subsequent line. Now you need to use the “copy” function to merge all the CSV files together. In a similar fashion to the “cd” command, type “copy” after the chevron, followed by a space then “combine.csv”. stacks to combine. The default setting is to combine the stacks horizontally, or side-by-side. The file chosen as “Stack 1” will be placed on the left of the resulting combined stack, and the file chosen as “Stack 2” will be placed on the right. If images are best combined vertically, the “Combine vertically” box can be selected. If you want to know which cells were measured by ImageJ, merge the original image with the outline image (‘Drawing of image…’). For this, invert the outline image by ‘Edit’ → ‘Invert’ . Open the original image again and use the menu command ‘Plugins’ → ‘RGB gray merge’.