I have some very large TIFFs (the smallest is ~80000x80000 pixels) of scanned cytology slides, and my goal is the automated extraction of cytometric features. This project must scale eventually, and so cannot require manual manipulation of each slide.
My language of choice is Python, but so far I’ve had limited success with the libtiff and OpenCV libraries or with the tifffile module due to the size of the images.
Even with the Fiji GUI I cannot open these images despite selecting “use virtual stack” or “crop on import.” I receive a Java error saying the array size is too large.
I’m unsure of how to proceed efficiently – but some important questions I have regard the basic structure of the files (series vs. planes vs. channels, etc.), how to scan over the image to perform segmentation, and how to get it all into Python. Is FIJI the correct tool for me?
Thanks in advance!