Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.1.0a4] - 2026-11-03

extract_ephys computes the LF RMS and power spectrum of NP2 recordings without an LF file from the AP file.

extract_ephys computes the RMS and power spectra on samples of the recording, in parallel, destripes the AP band before its RMS (which removes the LFP from the AP band of NP2 probes), and averages the power spectrum over windows rather than summing it.

extract_ephys saved the RMS and power spectra with the channels sorted by position on the probe rather than in file order, so NP2 plots showed the wrong channels. It now saves them in file order with a rawInd; recompute older files. Local files without rawInd that may be affected are reported when the session loads.
The raw data snippets and channel plots show each shank’s own channels, at their depth.
The image, scatter and probe plots are shown for sessions without xyz picks.
Colouring the slice channels by a probe plot failed, or used the wrong channels, when the spike sorting had fewer channels than the recording or listed them in another order.
Loading failed for a session YAML with a single multi-shank probe, for recordings shorter than 500 s, and for spike sorting without spikes.times, depths or amps.

The alignment model loads its own release (2026_W45) by default instead of the feature vintage it was trained on; the vintage now comes only from the release’s ephysatlas_model.json.
A local features file of another vintage than the model’s is refused, as Alyx features already were. The error names both vintages and how to resolve the mismatch.
The prediction panels have short titles, such as XGBoost prediction, in the GUI’s usual font.

After each fit, the depths of the reference line pairs along the probe and along the track, and the offset between them, are printed in the terminal (#17).
Channel prediction models in a new Prediction Plots menu (Alt+5), shown in a panel beside the ephys plots: two region decoders (XGBoost and ProbeTransformer) and an alignment model that aligns the recording to the histology track, with a result window and a confidence view. They are loaded from the Hugging Face Hub, and Shift+P shows all predictions side by side.
Documentation reorganised into tutorials, how-to guides, explanation and reference.

The Region Plots menu is renamed Set Mapping (Alt+M), and the chosen mapping applies to all histology panels.
The ephys-atlas features come with the session: the features dataset in the session YAML, a features file in the data folder, or Alyx online. The models run on the features of their own vintage. Without the ephysatlas extra the feature and prediction menus are hidden, and without features they are greyed out.
Session YAML: output must always be given, and raw_ephys no longer falls back to spike_sorting.

The RMS and Firing Rate image plots are drawn from the recording’s first timestamp rather than from 0 s, so they no longer appear blank when the recording does not start at 0 s (#15).
The configuration dropdown is offered for every session with two configurations, not only when the GUI is started with one: a two-configuration YAML opened from ... now shows it, and a single-configuration session hides it.
A session YAML with two configurations failed to load (KeyError on its first probe); both configurations and both are now offered in the configuration dropdown.
A session without spike sorting now opens, with the probe geometry read from the .ap.meta file in raw_ephys, which such a session must give; it used to fail on loading. The Filter Plots menu is greyed out without spike sorting.
Saving progress or uploading no longer fails when the output folder does not exist yet; it is created.

Plugins -> Channel Prediction -> Load features file…. The features come with the session: the YAML’s features dataset, a features file in the data folder, or the Alyx table online.

Channel prediction plugin, to predict channel location using inference or spatial encoding models (available by installing with ephysatlas extra).
Allen workflow for performing alignments in imaging space and reading and writing alignments to the Allen DocDB (available by installing with allen extra).
Save Progress (Shift+S), so an alignment that has not been uploaded can be recovered.
Region Plots menu (Alt+5) offering different region mappings.
Plots - raw LF plots, feature plots (with ephysatlas extra) and region plots (with ephysatlas extra).
Loading an insertion directly by id, with alignment-gui-ibl -p <pid>.
Documentation for the Channel Prediction plugin, the datasets and the keyboard shortcuts.

The package was reorganised: imports of app.app_controller, app.app_view, utils.utils and plugins.features_3d must be updated.
ibllib is now optional, installed with the ibl extra; offline mode runs without it.
3D viewer now uses ibl-datoviz as the backend
Data loading and plot building run on a background thread, with a progress dialog.

Probes read from were randomly ordered, now they are sorted alphabetically by name.
Sessions with no histology path in the YAML failed to load. Interpret as a session with no additional histology volumes.

The offset button has been removed, the same functionality can be achieved using a fit with a single reference line.