Derek Thirstrup

"no such column:class name" error message using classifier model in CellProfiler 4.2.1

4

I randomly get the following warning message when using a classifier model from CPA in a Cellprofiler pipeline. Can someone please help with this error? It stops the pipeline from...

upper and lower LUT sliders completely overlap[BUG]

3

**Describe the bug** The channel display LUT sliders overlap and can not be modified in many dim live cell images. Please add option to set values by actual pixel values...

How to specify device on A100 that is MIGed[INSTALL]

1

**Install problem** I am getting an error message when trying to run a script on our A100 linux nodes. The GPUs have been MIGed. I ran "export CUDA_VISIBLE_DEVICES='MIG-849e08aa-b1bd-5744-babc-e89e41b926b4'" to specify...

Using --no_norm with CLI slows down 3D segmentation[BUG]

1

The segmentation of 3d tif stacks is taking 5-6 minutes to process 1 image when --no_norm is used. When the same stacks are processed without --no_norm argument then it takes...

[BUG]Percentile normalization when norm3d=True

1

**Describe the bug** I wrote a script to denoise tif stacks using the new DenoiseModel class from Cellpose 3. It works great but there appears to be an issue with...

Multiscale ome zarr support

3

We are gearing up to release a large timelapse dataset that has been converted to ome-zarr format. We saved the data with multiscale zoom levels but this reader constantly defaults...

Missing watermark.pdf from Data Exploration step (version 1.1.5)

1

Run failed unexpectedly data-to-paper failed due to an unexpected error. --- no such file: 'C:\Users\derek\anaconda3\envs\data-to-paper\lib\site-packages\data_to_paper\latex\watermark.pdf' --- I was able to resolve this issue by copying the watermark.pdf from following github...

Cellpose-SAM excels at 3-D **inference**, but **training** still expects 2-D slices. This forces users to: * pre-slice every z-stack, losing volumetric anisotropic sampling context for learning model flow embeddings *...

Issue1038 Index error bugfix using tensor dimension checks, reshaping of tensor dimensions prevents out-of-range errors as well as additional dynamics.py performance optimizations

2

Resolve the following issues: Index error due to tensor dim mismatch and appears to minimize extra single pixel seeds often encountered in masks created with cellpose prior to 3.1.0 dynamics.py...

[BUG] Gaps in interphase and mitotic 3D nuclei when gradXY flows and cell probability look fine

2

I have found in my testing that the main branch Cellpose 4.0.6 has a bug where 3-D mask z slices can “disappear” in single or range of z-planes even when...