Closed tomkal closed 6 years ago
Hi there!
Thank you for the bug report, although this is the wrong place to report such bugs. This is the repository for the centrality estimation pipeline. Please, report bugs on the image analysis pipeline in the pygpseq repository.
The bug in question was reported yesterday by another user and is already fixed in version 3.0.2. It was caused by a wrong dependency setup (which can happen during the installation process) and is now fixed.
I would also suggest to use the -m
and -M
parameters (added from v3.0.0
) when running the pipeline, as they should speed up the segmentation process. Also, using the --compressed
flag will decrease the space occupied by the generated masks.
Check out the wiki for more details on how to run the latest versions of the pipeline.
Cheers
Before submitting an issue, please be sure to
git pull; sudo -H pip3 install .
)This issue affects
- [ ] Centrality estimation (
gpseqc_estimate
)What did you do (e.g., steps to reproduce)
I tried to run GPSeq microscopy pipeline.
What did you expect to happen?
To get beautiful YFISH plots as an output :)
What happened instead?
The pipeline failed by the segmentation step.
Additional information
My first action was to see if I am using the latest version of the pipeline. It happened to be already updated. Then, I took my previous data sets that I ran in the past and they failed at the same step. So the issue was not related to the images. I thought that maybe there was something fishy about them. Therefore, dear GG, maybe there is something silly from my side that I am doing wrong but at this point I do not know what could be the problem. Thanks! :)