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Published August 22, 2025 | Version v0.8.0
Software Open

NeuroConv

Description

v0.8.0 (August 21, 2025)

Removals, Deprecations and Changes

  • Segmentation writing pipeline no longer supports writing segmentation data without image or pixel masks PR #1400
  • Removed deprecated arguments: load_sync_channel in SpikeGLXNIDQInterface initialization and start_time, write_as and write_electrical_series in SpikeGLXNIDQInterface.add_to_nwbfile(). PR #1378
  • Removed starting_time as an argument from the recording interfaces add_to_nwbfile method and the stand alone add_recording_segment utility PR #1378
  • Deprecated the container_name parameter in ImageInterface.add_to_nwbfile() method. Use metadata_key in __init__ instead. This parameter will be removed on or after February 2026. PR #1439
  • Removed deprecated type aliases FolderPathType, FilePath, OptionalFilePath, and OptionalFolderPathType from utils. Use pydantic.DirectoryPath, pydantic.FilePath, or their optional variants directly. PR #1442

Bug Fixes

  • Fixed SpikeInterface physical unit properties being incorrectly included in electrodes table PR #1406
  • Fixed deprecated ROI extractor method calls: replaced get_image_size() with get_frame_shape(), get_num_frames() with get_num_samples(), and frame_slice() with slice_samples() in ophys interfaces PR #1443
  • Fixed logic bug in get_package function where boolean check was incorrectly compared to None PR #1477
  • Fixed docstring typos: corrected "default: Falsee" to "default: False" in multiple datainterface files PR #1472

Features

  • Segmentation interfaces now support roi ids that are strings PR #1390
  • Added InscopixImagingInterface for converting Inscopix imaging data. PR #1361
  • Added InscopixSegmentationInterface for converting Inscopix segmentation data. PR #1364
  • Added AxonRecordingInterface for converting extracellular electrophysiology data from Axon Binary Format (ABF) files with automatic session start time extraction PR #1413
  • Added FemtonicsImagingInterfacefor converting Femtonics imaging data. PR #1408
  • Added get_available_subjects static method to DeepLabCutInterface for extracting subject names from DeepLabCut output files PR #1425
  • Added MockPoseEstimationInterface for testing pose estimation workflows with deterministic Lissajous figure motion patterns PR #1435
  • Added IntanAnalogInterface for converting non-amplifier analog streams from Intan data files, supporting RHD2000 auxiliary input channels, RHD2000 supply voltage channels, USB board ADC input channels, and DC amplifier channels (RHS system only) PR #1440
  • Added metadata_key parameter to ImageInterface to allow custom naming and organization of image containers in NWB files. This enables multiple image interfaces to coexist with distinct container names. PR #1439
  • Added per-image metadata support to ImageInterface allowing users to specify individual resolution (pixels/cm), name and description for each image through metadata structure. PR #1441
  • Added rename_unit_ids() method to BaseSortingExtractorInterface for dictionary-based unit ID renaming, enabling clean handling of multiple sorting interfaces with overlapping unit IDs PR #1451
  • Added support for setting ProbeGroup objects in BaseRecordingExtractorInterface.set_probe() methodPR #1464
  • Added comprehensive tests for set_probe method in BaseRecordingExtractorInterface to verify probe and probe group functionality with proper electrode group organization in NWB files PR #1464
  • Added PyData Sphinx Theme version switcher to documentation navbar, enabling users to switch between stable (latest release) and main (development) versions PR #1478

Improvements

  • Added comprehensive FFmpeg video conversion how-to guide for converting bespoke video formats to DANDI-compatible formats PR #1426
  • Refactored Femtonics Imaging Interface session, munit and channel selection logic. PR #1433
  • Implemented PEP 735 dependency groups for test, docs, and dev dependencies PR #1434
  • Expanded test coverage for CaimanSegmentationInterface to include all stub files and added quality metrics properties (r_values, SNR_comp, cnn_preds) to the PlaneSegmentation table as segmentation_extractor_properties PR #1436
  • Added comprehensive how-to guide "Adding Multiple Sorting Interfaces" documenting approaches for handling multiple spike sorting outputs, including unit renaming strategies, separate processing tables, and adding custom properties for provenance tracking PR #1451 PR #1473
  • The copy button no longer copies the prompt (>>>) in the conversion gallery PR 1467

Notes

If you use this software, please cite it as below.

Files

catalystneuro/neuroconv-v0.8.0.zip

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