Mibi-bin-tools

You may download the latest release with:

shell
git clone -b v0.2.13 https://github.com/angelolab/mibi-bin-tools.git


What's new?

Spectral extraction

This is a feature that jranek experimented with to visualize the intensities across various spectral ranges on a pixel-by-pixel basis. Now that various different slides are being experimented with on the MIBI, it's proven especially useful when determining contaminants that have not previously needed to be included in the gold slide-based compensation matrix.

For each pixel, the intensities across each spectra observed in the range is returned in an X by Y by S array (S = spectra range). They can then be visualized across the entire image or certain subsections of the image (including individual pixels).

Specific visualization support will be added in a later release.

Licensing

An MIT license has been added for this repo. This officially makes it open source and free to use.

🚀 Features

- Adds total spectra extraction ackagel ([35](https://github.com/angelolab/mibi-bin-tools/pull/35))

📚️ Documentation

- MIT License srivarra ([67](https://github.com/angelolab/mibi-bin-tools/pull/67))
ackagel and srivarra

This latest patch introduces Python 3.12 support.

- Release v0.2.12, Python 3.12 Support srivarra ([65](https://github.com/angelolab/mibi-bin-tools/pull/65))
srivarra

This releases optimizes the computation of the median pulse heights across all masses at once (previously, it was a one-per-mass process). Additionally, fixes a bug in the time-of-flight range thresholding (see 62).

🚀 Features

- Parallelize histogram and MPH calculations alex-l-kong ([63](https://github.com/angelolab/mibi-bin-tools/pull/63))

📚️ Documentation

- Readme Adjustments, and Conda Environment file srivarra ([60](https://github.com/angelolab/mibi-bin-tools/pull/60))
alex-l-kong and srivarra

- Truncate the mass range to time-of-flight conversion to ensure consistent range extraction alex-l-kong ([56](https://github.com/angelolab/mibi-bin-tools/pull/56))
alex-l-kong

🚀 Features

- GitHub Actions Updates, and Python 3.9+ Support srivarra ([53](https://github.com/angelolab/mibi-bin-tools/pull/53))

🧰 Maintenance

- Next Release - v0.2.9 srivarra ([54](https://github.com/angelolab/mibi-bin-tools/pull/54))
srivarra