Sample image and/or code
I’ve edited downsampling to = 1 so there is no downsampling and image file format to .jpg
- This is a component_data.tif file (multilayer tif) that was generated after unmixing a multiplex scan from the Vectra 3. The .tif file when loaded into QuPath sees all appropriate 7 color channels with labels provided by the Vectra.
- Exporting in batch a set of images from a project with specific channels ON/OFF. For example, exporting DAPI and SOX10 only, without remaining multiplex FL channels
When running the script as “Run for Project (without save)” the two files I have in the test project export both as a tif and are not downsampled (great), however all channels in both images are still exported. I want only the 3 channels I have checked DAPI, CD33 and SOX10 that are seen in the image viewer to be exported into a single merged image.
I personally use HALO for all image analysis, however am needing an alternative simply for batch image export for specific channels. If ImageJ offers a better alternative to batch export multiplex images for certain channels, I’m all ears as well. Thank you!