Recently we’ve switched to image analysis of whole slide, stitched images using Qupath (currently still on m8). Our images range from 4GB to 20GB. Our setup to analyze these large images is as follows: images placed on a ‘network’ hard drive are analyzed by running Qupath on a server with 128GB of RAM and 8-2.4GHZ Xeon CPUs. Admittedly, the images are not stored locally to where Qupath is running.
We find two major issues:
- In images ~>10GB, cell segmentation does not occur. Qupath gets hung up and no tiling occurs.
- In most images, that have successfully cell segmented, Qupath will crash after poking around a bit at the cell measurements (for instance subcellular detections).
So my questions are:
- Any recommendations for a ‘better’ setup to handle these larger images? Our preliminary testing does show that a computer with tons of RAM and locally stored images does seem to work ‘better’. However, multiple users being able to easily access a server seemed appealing to us.
- Has anyone else found success with their own setup for handling large images?