Derek Thirstrup

I am also having this issue with CP 4.2.5. I have large brightfield 7401x7401 images that generates an estimated cell count for our celigo pipeline that worked fine in 4.2.1....

@carsen-stringer It appears to be fixed now in 3.0.6. I trained a label-free cell segmentation model so the image was a composite of brightfield and H2B endogenous EGFP channels. CP2...

@mrariden I have experienced this same issue. I get excellent results using the GUI with cellpose 2.2.2 when trained on a 1080 Ti for our lattice lightsheet data. However, I...

Yes it is a custom workflow with changes to a bunch of steps. I also included a hot pixel removal step at the end which is not part of any...

I built this ome zarr napari data loader which loads a csv of ome zarr filepaths via fire argument and uses bioio package for loading the volumetric image data. Bioio...

This bug is resolved in version 1.1.6. Thanks for fixing the issue.

I have also found extra single pixel objects in 3d masks with previous version of cellpose. I just made a PR for a bug fix to dynamics.py that fixes a...

@mrariden I have found the source of the missing z slices bug. I had to modify the dynamics.py file to tune a few of the variables used for filtering seeds...

Fix cellpose GUI flow visualization indexing and contrast bugs Summary This PR fixes critical bugs in cellpose GUI's flow visualization system that caused crashes and poor contrast in 3D datasets....

I have fixed this 3D indexing bug in gui.py and here is a link to the PR. https://github.com/MouseLand/cellpose/pull/1295/commits/b57d960f6a3c00e5af6f988d1380399d8639b897