v0.4.4 slow and unresponsive for 1GB TIF

[Mrc010]

Hi,

thanks for your interesting tool. I am having problems of the following kind:
When I load a 1GB image stack (TIF, resolution ~ 0.2x0.2x0.5 microns) and its corresponding masks (also 1GB TIF), the process is quite memory hungry (speaking of > 100GB) and loading takes hours. Also, when the loading process is eventually over, any interaction with the GUI make it unresponsive and memory consumption increases further w/o converging (I had to terminate when >400GB). So I suppose this tool is rather intended for smaller tissue patches with low double-digit lengths (in microns), or did I overlook something with respect to the input data?

[davidborland]

Yes, the tool has typically been used for much smaller volumes. Most of our data are 128x128x64 volumes (~2MB), with ~1000 cells per volume.

Unfortunately, I'm not surprised that there are performance issue for much larger volumes.

[kevinjohncutler]

I have the same issue. There are other programs that successfully load these image sizes (e.g. vispy/napari) without these memory issues, so optimization is certainly possible (but might be too much work to implement here).