I’m new to the large, batch processing of images world. I have liver tissue stained for CD3 (alexafluor 488), CD4 (alexafluor 555), and CD8 (alexafluor 660), as well as DAPI. I used an AxioScan microscope to scan the entire liver tissue sections and the output file type is .czi. What I would like to do is just quantify CD3+CD4+ and CD3+CD8+ area in each image. However the .czi files are really large and unwieldy, they’re about 1GB each. I’m wondering what plugins are available that could accomplish this task?
Any suggestions, tips, references, would be greatly appreciated.