Batch generation of multilayer tiff files and z-projection for 1-N IM04 datasets. The Perl script will parse all IM04 datasets within a user-specified directory and will generate a Fiji macro to process each unique entry (i.e. imaging coordinate ,or “Coordinate--Subposition--Loop—Colour”). The Fiji macro will subsequently generate colour specific subfolders within each experimental folder. For each “Coordinate--Subposition--Loop—Colour” entry, multilayer tiffs and z-projections are generated. CO6 (=bright field) data will be minimum z-projected, all other channels are maximum z-projected. Tested on Windows OS with Strawberry Perl (http://strawberryperl.com/). Please ignore the first version.

{"references": ["Pandey, Gunjan, et al. \"A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model.\" International journal of molecular sciences 20.6 (2019): 1290.", "Westhoff, Jens H., et al. \"Development of an automated imaging pipeline for the analysis of the zebrafish larval kidney.\" PLoS One 8.12 (2013): e82137."]}