Extracting and analysing MERFISH tif files into multiple channel images for better cellpose segmentation
- Convert from original .dax to .tif file
Dependencies:
- conda install -c conda-forge tifffile
- conda install -c anaconda numpy
python dax_converter.py input/path/with/.das_and_.inf/files
(Optional) copy files from original dir to the smaller dir with copy_files.sh
- Extraction of 3 border staining + DAPI
python extract_tiff_images.py --i /input/dir/with/.tif/files --o output/empty/dir
- Split 1 .tif into 4 different channels
python split_tif.py -i /input/dir/with/.tif/files/4_images -o output/empty/dir/for/splited/files
- Add colors and merge together
python merged_tif.py -i /input/dir/with/splited/files -o output/empty/dir/for/merged/files
- (Optional) add export annotation of masks into QuPath
- For the annotation script to work one need to create a project in QuPath, then paste it in automate > script editor > runs script (delete empty lines, because otherwise it will get an error)
export_annotation.groovy