callum-jpg

1. For declumping, I 100% agree that it should behave similarly to IDPrimary 2. I think the comparison of regional vs local is unfair in the attached notebook since it...

*"How do you square that with https://github.com/CellProfiler/CellProfiler/pull/4665#issuecomment-1479734311?"* It's definitely harder to reconcile this from that image alone. Since every regional maxima that we propose is can be determined by the...

The above pipeline was tested without the 16 footprint labelling of proposed seeds - sorry I didn't include this information. The same `scipy.ndimage.label` was used for both. I took a...

I performed some speed tests for regional vs local on either a distance transform or an intensity image. As was seen in the notebooks above, regional is faster for an...

Comparison of regional vs local on elongated bacteria. This aim of this test was to determine if regional can trace out much longer, non-cell-like objects outwith the provided footprint. **Regional...

I suppose a `threshold_image` function would be very similar to the from cellprofiler.library.modules function for `threshold`, which would take in all of the args and return the thresholded image

The potentially tricky part about not baking `_correct_local_threshold` ([link](https://github.com/CellProfiler/CellProfiler/blob/c6a6236dd487d94ffea493aef1d9e6e1a625b998/cellprofiler/modules/threshold.py#L1089)) into the `get_adaptive_threshold` is that the latter function involves `RectBivariateSpline`, which is used to 'smooth' out the blockiness of the adaptive...

These latest commits add discrete functions for global and adaptive thresholding, with a third functions that applies a threshold. 2D thresholds can also be applied like this: `thresh_img[thresh_img < threshold]...

> Minor detail - in general, it would be nice to inherit from the library modules in IDPrimary/Secondary rather than the module-modules (aka, Threshold). I'm guessing for Primary it would...

The hang here seems to occur at the for loop `for i, path in enumerate(paths)` in `cluster_paths_selection()`, which runs indefinitely. The paths for this image have been set incorrectly somehow....