Matt Einhorn

Support single z-stack tif file for input

6

## Description This is part of these other two PRs: https://github.com/brainglobe/brainglobe-workflows/pull/88 and https://github.com/brainglobe/brainglobe-utils/pull/67. **What is this PR** - [ ] Bug fix - [x] Addition of a new feature -...

Docs about updating or adding data

3

I'm looking at pynwb and how I can use it in our pipeline, but it's not exactly clear to me some of the data manipulation aspects as a user: *...

ENH: Allow linear_sum_assignment to accept a ufunc for very large graphs

3

### Is your feature request related to a problem? Please describe. We are trying to evaluate how different cell detection algorithms find cells. And so want to find the minimum...

jitclass doesn't use correct type for init arg

1

## Reporting a bug - [x] I have tried using the latest released version of Numba (most recent is visible in the release notes (https://numba.readthedocs.io/en/stable/release-notes-overview.html). - [x] I have included...

Move detection (2d/3d filtering, structure splitting) to PyTorch

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## Description **What is this PR** - [ ] Bug fix - [x] Addition of a new feature - [ ] Other **Why is this PR needed?** When I was...

I was using `BigStitcher` from `pyimagej` on Windows and needed to pass in paths. But, `BigStitcher` would choke on the paths claiming it can't find files there. I traced down...

Expose pin_memory to main and napari

2

## Description This depends on https://github.com/brainglobe/cellfinder/pull/542. **What is this PR** - [ ] Bug fix - [x] Addition of a new feature - [ ] Other **Why is this PR...

**Describe the bug** When installing any of the brainglobe packages, including cellfinder, as an editable install (`pip install -e .`), pip and python reports the wrong package version. As you...

Optimize data loading for cell classification

12

## Description This is still a WIP and needs a bit of polish. **What is this PR** - [ ] Bug fix - [x] Addition of a new feature -...

Add tiled thresholds to 2d filtering for determining foreground pixels

1

## Description This PR depends on https://github.com/brainglobe/cellfinder/pull/542. Also, the figures below were generated using https://github.com/brainglobe/cellfinder/pull/544. This adds a tiled threshold to the 2d filtering step that decides whether a pixel...