Allensdk

Bug Fixes
- (Internal) Fixed a bug in mesoscope processing where the ophys acquisition frames were being truncated
prior to splitting, resulting in many fewer than expected acquisition frames.

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.

Bug Fixes
- (Internal) Fixed a write\_nwb bug for behavior ophys experiments involving the BehaviorOphysJsonApi expecting a mesoscope-specific method.

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.

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

Added
- Behavior Ophys NWB File writing capability fixes for updated PyNWB and HDMF versions
- Added warning if using outdated Visual Coding Neuropixels NWB files
- Added documentation file for Visual Behavior terms in AllenSDK for quick lookup