I’m pleased to announce the existence of some very useful software that uses CellProfiler under the hood: Orbit Image Analysis. It’s designed to handle huge whole-slide scans of, for example, tissue samples. https://www.orbit.bio/
You can do pixel-based machine learning to identify the proportion of the image occupied by certain cell types. You can do simple segmentation within the software or you can mark regions of interest and export tiles within that region to analysis by CellProfiler. Configure your CP pipeline however you like and apply it to regions of interest that are too large to be handled in CP’s memory at once.
For best use, it requires you deposit your images into OMERO (performance is very slow otherwise). We don’t have any hands-on experience with it here on the team but we wanted to let people know right away so we can hear your feedback on it and whether it solves all your large-format image problems. Give it a try and tell the community what you think!