int-brain-lab / ibleatools / 39674323354
51%

DEFAULT BRANCH: main
Ran
Jobs 1
Files 65
Run time 1min
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
coverage: 48.577% (-7.5%) from 56.103%
39674323354

push

github

web-flow 
Interp/2c probe alignment (#147)

* ephysatlas.alignment: histology-based and ephys-only probe localization

- align_histology warps a probe's recorded channel features along its reconstructed histology
  trace onto the channel-level model's predictions (dynamic time warping);
  align_histology_with_units adds the unit-level likelihood under the sub-type mixture.
- EphysOnlyLocalizer / localize_ephys_only search for the probe without histology (Student-t
  likelihood and a planned-trajectory prior).
- ChannelModel / UnitModel load the published releases with load_pretrained.
- plot_alignment_result shows what a user aligning a new recording has: the histology trace,
  planned trajectory and inferred alignment, the cost matrix with its warping path, and the
  region, confidence and feature stripes.
- scripts/run_alignment_heldout.py and scripts/run_alignment_dataset.py run the held-out
  evaluation and the dataset-wide flags.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* alignment: default to the 2026_W42 channel-level release

The channel-level model retrained on the 2026_W42 feature release (the *_bpr features with
the ibl-neuropixel 1.14 Cadzow denoising) and the refreshed alignments, on the probe split
and context volumes of 2026_W41. Held-out mean R2 0.385 (2026_W41: 0.380) on the same 151
test insertions. The unit-level release stays 2026_W42, trained on the 2026_W41 units.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* CHANGELOG: ephysatlas.alignment and the 2026_W42 release

* docs: add the 2026_W42 encoding volume to the vintage table

---------

Co-authored-by: asaguy <as7709@columbia.edu>
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

4625 of 9521 relevant lines covered (48.58%)

0.49 hits per line

Jobs
ID Job ID Ran Files Coverage
1 39674323354.1 65
48.58
GitHub Action Run
Source Files on build 39674323354