v0.2.3

You may download the latest release with:

git clone -b v0.2.3 https://github.com/angelolab/ark-analysis.git

What's new?

Noodle range extraction fix

Previously, users had run into issues with extremely dim Noodle signal. This was caused by an incorrect extraction range, which has been corrected by updating the range in the panel file of the cohort. With this correction, commercial_rosetta_matrix_v1.csv has again become the default matrix to use, as the _v2 matrix was applied over the incorrectly-extracted Noodle channel.

Backward compatibility for panels with incorrect Noodle ranges at the time of extraction has also been added.

Batch effects across TMAs

The batch effects notebook has been generalized to provide summary statistics across all TMAs. This can help isolated systematic issues that may occur across different TMA slides.

Autogain support

Ionpath has introduced the autogain feature, which reduces (but does not completely eliminate) the need for normalization. Additional visualization tools and support are implemented in this release to support this new functionality. Backward compatibility for non-autogain runs is also in place.

Temporary alpineer hotfixes

Due to changes in alpineer to support updates by @bryjcannon to support ezSegmenter and generic masks in ark-analysis, some breaking changes were introduced to toffy. While alpineer gets updated, temporary changes have been made to ensure compatibility.

Rosetta tiling fixes

In some unusual cases, Rosetta tiling will fail due to a divide-by-zero error in case of extremely sparse signal. A patch has been added for this case.

🚀 Features

• Bump commercial Rosetta matrix to v2 @alex-l-kong (#460)
• Adjust the batch effect QC notebook to average stats across all TMAs @camisowers (#458)
• Prevent pulse_height_fit from throwing dtype warning with floats @alex-l-kong (#456)
• Add support for MIBI runs acquired using autogain feature @alex-l-kong (#455)
• For autogain runs, add voltage plotting scheme @alex-l-kong (#453)

🐛 Bug Fixes

• Normalize by maximum pixel in case of Rosetta tiling for sparse signal @alex-l-kong (#472)
• Support legacy panel files defined before the Noodle range extraction fix @alex-l-kong (#470)
• Enforce exact_match=True when listing JSON file for get_estimated_time for MPH @alex-l-kong (#467)
• Fix Noodle extraction range in convert_panel() @camisowers (#464)
• Normalization notebook bug @camisowers (#461)

🧰 Maintenance

• Release v0.2.3 @alex-l-kong (#476)
• Bump mibi-bin-tools to 0.2.14 @alex-l-kong (#475)

📚️ Documentation

• Fix normalization documentation @camisowers (#454)

@alex-l-kong, @camisowers, and @srivarra