Beth Cimini

Fix renumbering when using different objects as neighbors

1

Resolves #4928

Neighbor numbers wrongly reported when objects and neighbors are different

1

H/T [the forum](https://forum.image.sc/t/measureobjectneighbors-module-not-giving-the-desired-neighbor-object-number/99876/4) --- **Describe the bug** Because users can optionally decide that, when running MeasureObjectNeighbors, they want to keep object distances to objects that were thrown out for touching...

Add local thresholding catch for all nans or a mixture of 0s and nans

2

Resolves #4862 Leaving as draft for now because we probably want a test here

In 2D and in fixed 3D (pending PRs), the table isn't grabbing the size correctly, so when it first comes up, the table overlaps the images. Resizing the window fixes...

When using Runilastik on an ilastik project file that was trained with multichannel input, even if we give it the same/correct image, it barfs. I suspect it's an ordering issue...

Can't install on M1 Mac, Python 3.9

1

Stack trace below, for both Cython 3 and 0.29.37 Cython3 ``` pip install python-javabridge Collecting python-javabridge Using cached python-javabridge-4.0.3.tar.gz (1.3 MB) Preparing metadata (setup.py) ... done Requirement already satisfied: numpy>=1.20.1...

"Soft warning"/caution implementation

1

**Is your feature request related to a problem? Please describe.** There are many things in CellProfiler where one _can do_ something (like, say, set a threshold correction factor of 20),...

When running batch files, DCP passes in `pipeline` and `-i`, but not `--data-file` (because it shouldn't need it because path info is in the batch file). HOWEVER, apparently in this...

Spot instance not joining the cluster when ASSIGN_IP = False

2

Kamal ran into an issue where his spot instances were not joining the cluster with ASSIGN_IP=False; setting it to true made the instances appear in the cluster again. So something...