I have acquired confocal Z-stack images of skin where I would like to analyze only cells that are located in the stroma, but not in the epidermis and the hair follicles. To do this, I have made a binary mask for every Z-stack image, which I would like to use to mask every Z level of the specific Z-stack.
I have already managed to do this with one Z-stack and its mask by using the NamesAndTypes module and importing the mask as a single image. Together with extracting metadata from the image file headers, it nicely separates the different Z-levels and masks them all.
What I would like to do is to use a similar approach for about 40 Z-stacks and their masks at the same time, but I haven’t found a way of doing it in a single step.
I have tried using image rules to separate my Z-stacks and their masks (file ends with mask), but this results in the output of a single image.
Is there a way I could import all of my Z-stacks and masks in one step and then use the masks for every Z-level?
The representative pipeline where I get this problem and a couple of sample images and masks can be found here (for some reason I wasn’t able to upload them directly, even when compressed to .zip):
Thanks for the help!
Edit: I added an example pipeline to the folder that imports a single image - this works for one Z-stack, but not multiple.