v2.4.1

Merge pull request #1806 from AllenInstitute/bugfix/deprecated-scipy-…

v2.4.0

Merge pull request #1744 from AllenInstitute/rc/2.4.0

rc/2.4.0

v2.3.2

Bug Fixes

• (Internal) Fixed a running_processing bug for behavior ophys experiments when the input data would have one more encoder entry than timestamp. The behavior of the code now matches what the warning says.

v2.3.1

Bug Fixes

• (Internal) Fixed a write_nwb bug for behavior ophys experiments involving the BehaviorOphysJsonApi expecting a mesoscope-specific method.

v2.3.0: Merge pull request #1703 from AllenInstitute/rc/2.3.0

Added

• Adds load sync data for individual plane sets to relate accurate event timings to mesoscope data.
• Adds public API method to access the behavior_session_id from an instance of BehaviorOphysSession.

Changes

• Visual behavior running speed is now low-pass filtered at 10Hz. The raw running speed data is still available. The running speed is corrected for encoder threshold croissing artifacts.
• Support for stimulus gratings for visual behavior.
• Updates to some visual behavior pynwb implementations.

Bug Fixes

• Fixed an eye-tracking sync problem.

v2.2.0

Added

• AllenSDK HTTP engine streaming requests now include a progress bar.

Changed

• (Internal) Behavior Ophys Sessions no longer have a dependence on the segmentation_mask_image file (provided by LIMS) when trying to write NWB files.

Bug Fixes

• (Internal) response_time of a trial in behavior-only or behavior + ophys sessions is now the first lick of the trial (for non-"aborted" trials). If no lick occurred or if the trial is "aborted", response_time is NaN.
• Resolve ImportError: cannot import name 'MultiContainerInterface' from 'hdmf.container' errors by removing explicit version bounds on the hdmf package.
• The optical physiology 2-photon trace demixer has been modified to be more memory friendly and should no longer result in out of memory errors when trying to demix very large movie stacks.
• (Internal) Docker image definitions have been updated so that internal continuous integration tests can work properly

v2.1.0

Added

• Added warning if using outdated Visual Coding Neuropixels NWB files
• Added documentation file for Visual Behavior terms in AllenSDK for quick lookup

Bugfixes

• (Internal) Behavior Ophys NWB file writing capability fixes for updated PyNWB and HDMF versions

v2.0.2 (Internal Bugfix)

Bug Fixes

• Fixes failure in plotting method used by internal data pipeline code (OPHYS_DEMIX_QUEUE)

v2.0.1

Bug Fixes

• Update version requirements for pynwb and hdmf

AllenSDK 2.0.0

Added

• CCF locations for ecephys neuropixels electrodes have been added to their respective nwb electrodes tables
• Examples for accessing eye tracking ellipse fit and screen gaze location data have been added to ecephys example notebooks

Changed

• pynwb and hdmf version pinning has been relaxed
• The organization of data for ecephys neuropixels Neurodata Without Borders (NWB) files has been significantly changed to conform with NWB specifications and best practices

Important Note:
Due to newer versions of pynwb/hdmf having issues reading previously released Visual Coding Neuropixels NWB files and due to the significant reorganization of their NWB file contents, this release contains breaking changes that necessitate a major version revision. NWB files released prior to 6/11/2020 are not guaranteed to work with the 2.0.0 version of AllenSDK. If you cannot or choose not to re-download the updated NWB files, you can continue using a prior version of AllenSDK (< 2.0.0) to access them. However, no further features or bugfixes for AllenSDK (< 2.0.0) are planned.

Data released for other projects (Cell Types, Mouse Connectivity, etc.) are NOT affected and will NOT need to be re-downloaded

Addendum:
Please note that when getting Visual Coding Neuropixels stimulus presentations for this new version of AllenSDK that some columns have been removed due to their uninformative or superfluous nature.

# The `colorSpace`, `depth`, `interpolate`, `pos`, `rgbPedestal`,
# `tex`, `texRes`, `flipHoriz`, `flipVert`, `rgb`, `signalDots`
# are now omitted in the stimulus table.
stimulus_table = session.get_stimulus_table()