Recent Releases of https://github.com/alleninstitute/allensdk
https://github.com/alleninstitute/allensdk - v2.16.2
What's Changed
- ticket/PSB-260: Bug fix to VBN by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2731
- Rc/2.16.2 by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2738
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.16.1...v2.16.2
- Jupyter Notebook
Published by morriscb over 2 years ago
https://github.com/alleninstitute/allensdk - v2.16.1
What's Changed
- rc/2.16.1 by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2735
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.16.0...v2.16.1
- Jupyter Notebook
Published by morriscb over 2 years ago
https://github.com/alleninstitute/allensdk - v2.16.0
What's Changed
- Ticket/psb-171: Various fixes for VBO release by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2707
- Update Dependency Compatibility by @mikejhuang in https://github.com/AllenInstitute/AllenSDK/pull/2716
- Ticket/PSB-167: Add quality to metadata table by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2712
- ticket/PSB155: Add isshamchange column. by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2715
- Fix for namespaces issue by @brendanjohnharris in https://github.com/AllenInstitute/AllenSDK/pull/2714
- unpin hdmf and pynwb by @mikejhuang in https://github.com/AllenInstitute/AllenSDK/pull/2720
- ticket/PSB-200: Clean up rc/2.16.0 by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2721
- ticket/PSB-227: Revert to json for vbn packaging. by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2723
- Ticket/PSB-235: Fixes needed for data release by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2724
- Ticket/PSB-207: by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2726
- ticket/PSB-257: Investigate AllenSDK test failure for python3.9 by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2729
- Ticket/PSB-249: Address comments on final release candidate. by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2728
- Ticket/PSB-7 by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2730
- Rc/2.16.0 by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2722
New Contributors
- @brendanjohnharris made their first contribution in https://github.com/AllenInstitute/AllenSDK/pull/2714
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.15.2...v2.16.0
- Jupyter Notebook
Published by morriscb over 2 years ago
https://github.com/alleninstitute/allensdk - v2.15.2
What's Changed
- update VBO read the docs page by @matchings in https://github.com/AllenInstitute/AllenSDK/pull/2660
- fixes issue with loading trials from BehaviorEcephysSession.from_nwb by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2701
- ticket/PSB-134: Unpin statsmodels by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2699
- ticket/PSB-173: Create allensdk_anaconda3 image in Pika dockerhub. Modify Bamboo script by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2708
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.15.1...v2.15.2
- Jupyter Notebook
Published by morriscb almost 3 years ago
https://github.com/alleninstitute/allensdk - v2.15.1
What's Changed
- rc/2.15.1: HOTFIX by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2652
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.15.0...v2.15.1
- Jupyter Notebook
Published by morriscb over 3 years ago
https://github.com/alleninstitute/allensdk - v2.15.0
What's Changed
- Remove to_json from data objects and their associated tests by @mikejhuang in https://github.com/AllenInstitute/AllenSDK/pull/2626
- Modify write nwb methods to instantiate objects using from_lims by @mikejhuang in https://github.com/AllenInstitute/AllenSDK/pull/2624
- Vco eye tracking by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2639
- Ticket-2541: Add project code to several locations. by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2623
- ticket:PSB-19: Fixup typing by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2642
- Vbn lfp behavior tutorials by @corbennett in https://github.com/AllenInstitute/AllenSDK/pull/2640
- Update Data changes for VBN. by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2649
- Add targetedimagingdepth column to getophysexperiment_table by @mikejhuang in https://github.com/AllenInstitute/AllenSDK/pull/2648
- ticket/PSB-24: Modify Age data_object to calculate mouse age at the date of aquisition of session. by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2644
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.14.1...v2.15.0
- Jupyter Notebook
Published by aamster over 3 years ago
https://github.com/alleninstitute/allensdk - v2.14.1
What's Changed
- Fix issues with notebooks by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2635
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.14.0...v2.14.1
- Jupyter Notebook
Published by aamster over 3 years ago
https://github.com/alleninstitute/allensdk - v2.14.0
- Support for updated vbn release containing probe, lfp and behavior only data.
- Updates to Ophys data in anticipation of a forthcoming updated data release
- Various notebook updates
- Python 3.9 support
- Various bug fixes and quality of life improvements.
- Jupyter Notebook
Published by morriscb over 3 years ago
https://github.com/alleninstitute/allensdk - v2.13.8
What's Changed
- Fixes dataframe indices by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2580
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.13.7...v2.13.8
- Jupyter Notebook
Published by aamster over 3 years ago
https://github.com/alleninstitute/allensdk - v2.13.7
What's Changed
- Update vbn notebooks by @corbennett in https://github.com/AllenInstitute/AllenSDK/pull/2523
- Update vbn quality metrics tutorial by @corbennett in https://github.com/AllenInstitute/AllenSDK/pull/2528
- Fix bug because LIMS is passing old version of stimulus presentations table to current source density module https://github.com/AllenInstitute/AllenSDK/commit/0223f6d8c8a6fb62ca732a7fca180a1d189a3dd1
New Contributors
- @corbennett made their first contribution in https://github.com/AllenInstitute/AllenSDK/pull/2523
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.13.6...v2.13.7
- Jupyter Notebook
Published by aamster over 3 years ago
https://github.com/alleninstitute/allensdk - v2.13.6
What's Changed
- Fixes issue with accessing stimulus presentations table of released v… by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2509
- VBN notebook updates by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2511
- Rc/2.13.6 by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2512
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.13.5...v2.13.6
- Jupyter Notebook
Published by aamster almost 4 years ago
https://github.com/alleninstitute/allensdk - v2.13.5
What's Changed
- Speed up loading of stimulus presentations table from NWB 2.0 files by @jsiegle in https://github.com/AllenInstitute/AllenSDK/pull/2313
- Issue/2304/genotype/is/none by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2318
- Fix monitor delay bug by @sgratiy in https://github.com/AllenInstitute/AllenSDK/pull/2316
- moves data object base classes out of behavior by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2335
- ticket/nnnn/sync/stim/aligner by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2354
- Create VBN EyeTracking data object by @sgratiy in https://github.com/AllenInstitute/AllenSDK/pull/2355
- Probes data object by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2356
- Adds optotagging table data object by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2359
- ticket-2341: Create VBN Licks data object by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2360
- Makes Presentations class compatible with VBN by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2361
- Add ability to write stimulus templates to NWB for VBN by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2362
- add behavior ecephys metadata by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2363
- Ticket/2357/multi/stim/timestamps by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2364
- ticket/2337/multi/stim/running/speed by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2368
- Behavior ecephys session by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2367
- Ticket/2370/lick/timestamps by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2373
- Vbn nwb writer by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2372
- Ticket/2375/eye/tracking/timestamps by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2378
- ticket/nnnn/get units/bug by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2381
- Removes unnecessary validation on non-behavior files by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2389
- Fix reporter line by @sgratiy in https://github.com/AllenInstitute/AllenSDK/pull/2390
- ticket/2383/lick/timestamps by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2392
- Makes sure timestamps and eye tracking frames are aligned by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2397
- Removes dependency on hardcoded acronym-id map and strips subregion from acronym by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2401
- Fixes issue with nan manualstructureacronym by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2404
- Update further documentation link by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2398
- ticket/ecephys/33a/metadata/writer by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2407
- Ticket/2412/read/pickle/file by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2426
- Create VBN project cache by @sgratiy in https://github.com/AllenInstitute/AllenSDK/pull/2419
- Ticket/2433/vbo/bug by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2434
- Ticket/2400/vbn/input/jsons by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2438
- Ticket/2428/filter sessions by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2430
- Ticket/2416/date/of/acq by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2440
- Ticket/2432/rename/local index by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2444
- Ticket/2443/missing/sessions by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2449
- Ticket/2450/supplemental/columns by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2451
- Ticket/2453/bad/mouse by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2455
- Memory leak by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2465
- Ticket/2454/rename/vbn/fields by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2462
- tolist() can be expensive; use list comprehension instead which is fas… by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2468
- Vbn 2022 dev by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2435
- Ticket/2467/trials/times by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2469
- Ticket/2371/vbo/access by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2474
- Vbn/access by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2476
- increase lower bound on jinja2 by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2481
- ticket-2464: Modify loading projection image to get correct data from lims. by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2479
- Docstring/type hint improvements to VisualBehaviorNeuropixelsProjectCache by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2482
- BehaviorSession.from_lims now supports checking if eye tracking metad… by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2483
- reads session type from pkl file instead of from mtrain by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2488
- adds leftrightccf_coordinate to project level units table by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2489
- after pynwb update from 2.01 to 2.1.0, the defaults on the electrode … by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2493
- fix test by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2494
- Adds support for VBN trials table having different name for 'change_time' by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2495
- rename autorewarded to auto_rewarded in rewards table by @aamster in https://github.com/AllenInstitute/AllenSDK/pull/2498
- Ticket/2470/vbn/documentation by @danielsf in https://github.com/AllenInstitute/AllenSDK/pull/2471
- rc/2.13.5 by @morriscb in https://github.com/AllenInstitute/AllenSDK/pull/2309
Full Changelog: https://github.com/AllenInstitute/AllenSDK/compare/v2.13.4...2.16.0
- Jupyter Notebook
Published by aamster almost 4 years ago
https://github.com/alleninstitute/allensdk - v2.13.2
- Fixes bug that caused file paths on windows machines to be incorrect in Visual behavior user-facing classes
- Updates to support MESO.2
- Loosens/updates required versions for several dependencies
- Updates in order to generate valid NWB files for Neuropixels Visual Coding data collected between 2019 and 2021
- Jupyter Notebook
Published by aamster over 4 years ago
https://github.com/alleninstitute/allensdk - v2.13.0
- Major internal refactor to
BehaviorSession,BehaviorOphysExperimentclasses. ImplementsDataObjectpattern for fetching and serialization of data.
- Jupyter Notebook
Published by aamster over 4 years ago
https://github.com/alleninstitute/allensdk - v2.12.3
Changes: - Reorder Visual Behavior metadata columns to be more helpful
- Jupyter Notebook
Published by njmei almost 5 years ago
https://github.com/alleninstitute/allensdk - v2.12.2
- Jupyter Notebook
Published by djkapner almost 5 years ago
https://github.com/alleninstitute/allensdk - v2.12.1
minor fix to cloud cache
- Jupyter Notebook
Published by djkapner almost 5 years ago
https://github.com/alleninstitute/allensdk - v2.12.0
Released 2021-08-11
- Added ability to specify a static cache directory (usestaticcache=True) to instantiate VisualBehaviorOphysProjectCache.fromlocalcache()
- Added 'experiencelevel', 'passive' and 'imageset' columns to ophysexperimentstable
- Added 'ophyscellstable' metadata table to track the relationship between ophysexperimentid and cellspecimenid
- Jupyter Notebook
Published by djkapner almost 5 years ago
https://github.com/alleninstitute/allensdk - v2.11.3
- Jupyter Notebook
Published by djkapner almost 5 years ago
https://github.com/alleninstitute/allensdk - v2.11.2
- Jupyter Notebook
Published by djkapner about 5 years ago
https://github.com/alleninstitute/allensdk - v2.11.1
Refactored the schema for the ecephys copy utility to avoid raising an error when a previous output file already exists.
- Jupyter Notebook
Published by Matyasz about 5 years ago
https://github.com/alleninstitute/allensdk - v2.11.0
- python 3.8 compatibility
- CloudCache (the class supporting cloud-based data releases) is now smart enough to construct symlinks between files that are identical across dataset versions (rather than downloading duplicate copies of files).
- VisualBehavioOphysProjectCache supports user-controlled switching between dataset versions.
- Jupyter Notebook
Published by Matyasz about 5 years ago
https://github.com/alleninstitute/allensdk - v2.10.3
Adds restriction to require hdmf version to be strictly less than 2.5.0 which accidentally introduced a major version breaking change
- Jupyter Notebook
Published by Matyasz about 5 years ago
https://github.com/alleninstitute/allensdk - v2.10.2
This version marks the release of Visual Behavior Optical Physiology data! For more details please visit the: Visual Behavior - Optical Physiology Project Page
Other changes: - update documentation to support visual behavior data release - Fixes a bug with the dictionary returned by BehaviorSession get getperformancemetrics() method - Adds docstrings to the BehaviorSession getperformancemetrics(), getrollingperformancedf(), and getreward_rate() methods
- Jupyter Notebook
Published by djkapner about 5 years ago
https://github.com/alleninstitute/allensdk - v2.10.1
- Jupyter Notebook
Published by djkapner about 5 years ago
https://github.com/alleninstitute/allensdk - v2.9.0
- Jupyter Notebook
Published by djkapner over 5 years ago
https://github.com/alleninstitute/allensdk - v2.8.0
- Jupyter Notebook
Published by djkapner over 5 years ago
https://github.com/alleninstitute/allensdk - v2.7.0
- Jupyter Notebook
Published by djkapner over 5 years ago
https://github.com/alleninstitute/allensdk - v2.6.0
- Jupyter Notebook
Published by djkapner over 5 years ago
https://github.com/alleninstitute/allensdk - v2.5.0
- Jupyter Notebook
Published by djkapner over 5 years ago
https://github.com/alleninstitute/allensdk - v2.4.1
- Jupyter Notebook
Published by djkapner over 5 years ago
https://github.com/alleninstitute/allensdk - v2.4.0
- Jupyter Notebook
Published by djkapner over 5 years ago
https://github.com/alleninstitute/allensdk - 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.
- Jupyter Notebook
Published by Matyasz over 5 years ago
https://github.com/alleninstitute/allensdk -
Bug Fixes
- (Internal) Fixed a write_nwb bug for behavior ophys experiments involving the BehaviorOphysJsonApi expecting a mesoscope-specific method.
- Jupyter Notebook
Published by Matyasz over 5 years ago
https://github.com/alleninstitute/allensdk -
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.
- Jupyter Notebook
Published by djkapner over 5 years ago
https://github.com/alleninstitute/allensdk - 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_imagefile (provided by LIMS) when trying to write NWB files.
Bug Fixes
- (Internal)
response_timeof 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_timeisNaN. - Resolve
ImportError: cannot import name 'MultiContainerInterface' from 'hdmf.container'errors by removing explicit version bounds on thehdmfpackage. - 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
- Jupyter Notebook
Published by njmei almost 6 years ago
https://github.com/alleninstitute/allensdk -
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
- Jupyter Notebook
Published by njmei almost 6 years ago
https://github.com/alleninstitute/allensdk - v2.0.1
Bug Fixes
- Update version requirements for pynwb and hdmf
- Jupyter Notebook
Published by kschelonka almost 6 years ago
https://github.com/alleninstitute/allensdk - v2.0.2 (Internal Bugfix)
Bug Fixes
- Fixes failure in plotting method used by internal data pipeline code (OPHYSDEMIXQUEUE)
- Jupyter Notebook
Published by kschelonka almost 6 years ago
https://github.com/alleninstitute/allensdk - 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.
stimulustable = session.getstimulus_table() ```
- Jupyter Notebook
Published by njmei about 6 years ago
https://github.com/alleninstitute/allensdk -
- added getreceptivefield alias() for getrf() in allensdk/brainobservatory/ecephys/stimulusanalysis/receptivefieldmapping.py
- Added required version to namespace and caches spec in ecephy nwb outputs in allensdk/brainobservatory/ecephys/nwb/AIBSecephys_namespace.yaml
- Added version for ophys behavior nwb output to allensdk/brainobservatory/nwb/AIBSophysbehaviornamespace.yaml
- Behavior and ECEphys project caches no longer accept arbitrary keywords to prevent confusion when user supplies incorrect kwargs to constructor.
- New ecephys notebook for optotagging tutorial.
- Jupyter Notebook
Published by njmei about 6 years ago
https://github.com/alleninstitute/allensdk - v1.8.0
v1.8.0
Added
- The biophysical module can now run both current and legacy all-active models.
- Internal users can now access
date_of_acquisitionfor behavior-only Session data. - A pull request template was added to the repository.
Changed
- The CSV log was removed from
BehaviorProjectCache(internal users). - Duplicated demixer module was deprecated, and test coverage was added.
- Docker image for AllenSDK was updated.
Bug Fixes
- Internal LIMS data served to
BehaviorDataSessionclass now all use the same timestamp source
- Jupyter Notebook
Published by kschelonka about 6 years ago
https://github.com/alleninstitute/allensdk - Bug fix testing in AllenSDK
Bug Fixes
- Removal of old calls to mock return objects that no longer exist
- Moving from old test endpoint to production endpoint for testing
- Jupyter Notebook
Published by isaak-willett about 6 years ago
https://github.com/alleninstitute/allensdk - v1.7.0
Added
- Internal users can now access
eye_trackingellipse fit data from behavior + ophys Session objects - A new mixin for managing processing parameters for Session objects
- Added support for additional sync file line labels
Changed
- Monitor delay calculation is updated to properly handle photodiode streams that end on a rising edge. We are no longer providing a default delay value in case of error.
Bug Fixes
- experiment_table from behavior project cache has NaNs in the 'imaging_depth' column for MultiScope experiments due to incorrect join in behavior_project_lims_api.py and 4 other places where ophys_sessions was incorrectly queried for imaging_depth_id
- get_keys method for sync datasets was returning the wrong line labels and creating incorrect key, value pairs for data loading from sync files
- Jupyter Notebook
Published by isaak-willett about 6 years ago
https://github.com/alleninstitute/allensdk - v1.5.0
What's New - 1.5.0 (February 21, 2020)
Added
- Users have an option to provide credentials for accessing the database either explicitly via public API or by setting up the environment variables
Changed
- Allow users to modify BehaviorDataSession and BehaviorOphysSession data
Bug Fixes
- morphology.apply_affine correctly rescales radii
- invalid extracellular electrophysiology spikes no longer show up as spikes at time -1
- (internal) When loading a behavior session, behavior and eye tracking video frame times are assessed from the correct lines
- Jupyter Notebook
Published by NileGraddis over 6 years ago
https://github.com/alleninstitute/allensdk - v1.4.0
As of the 1.4.0 release:
- users of the ephys extractor can supply their own cutoff frequency for low-pass bessel filter.
- (internal feature) the ophys time sync module writes an output json describing its results.
- Jupyter Notebook
Published by NileGraddis over 6 years ago
https://github.com/alleninstitute/allensdk - v1.3.0
What's New - 1.3.0 (December 12, 2019)
The 1.3.0 release adds
- Improved Neuropixels data download performance by enabling asynchronous transfers. Users can now also specify a timeout and number of retries when downloading data.
and fixes
- Hanging downloads for Neuropixels NWB files
- Updated AllenSDK readme and contributing documentation
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Published by njmei over 6 years ago
https://github.com/alleninstitute/allensdk -
The 1.1.1 release adds
- several new Visual Coding - Neuropixels example notebooks
and fixes
- a bug in which pvaluerf and onscreenrf were swapped when accessed from an EcephysSession
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Published by njmei over 6 years ago
https://github.com/alleninstitute/allensdk - v1.2.0
What's New - 1.2.0 (November 21, 2019)
The 1.2.0 release adds
- (internal feature) A project cache for the Behavior Ophys project, with example notebook
- (internal feature) A major overhaul of the BehaviorOphysLimsApi
- (internal feature) Updates to the EcephysProjectLimsApi such that it returns data in the same format as the EcephyProjectWarehouseApi
- improved eye-tracking area calculation
and fixes
- several flaky tests
- regress tests which depend on scipy's ks_2samp
- (internal feature) duplicate caching on the Bevavior Ophys Lims Api
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Published by NileGraddis over 6 years ago
https://github.com/alleninstitute/allensdk -
What's New - 1.0.2 (October 14, 2019)
The 1.0.2 release brings support for the Allen Brain Observatory - Visual Coding Neuropixels dataset! This dataset is a large-scale extracellular electrophysiological survey of mouse subcortical visual cortical regions using high-density neuropixels probes.
To get started with these data, see the Visual Coding - Neuropixels section
We have implemented new and improved eye-tracking methods based on Deep Lab Cut. These eye tracking results can be accessed for existing brain observatory experiments by calling get_ophys_eye_gaze_data on a BrainObservatoryCache object. For Neuropixels sessions, you can access these data by calling get_eye_tracking_data on an EcephysSession object.
With this release, we are no longer supporting Python 2.
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Published by njmei over 6 years ago
https://github.com/alleninstitute/allensdk -
What's New - 1.1.0 (October 31, 2019)
The 1.1.0 release adds: - an updated gaze mapping algorithm - automatic retries for failed neuropixels NWB file downloads
and fixes:
- several failing nightly build tests
- warnings emitted due to use of deprecated h5py.Dataset.value
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Published by njmei over 6 years ago
https://github.com/alleninstitute/allensdk - Release 0.16.3
Bug Fixes - https://github.com/AllenInstitute/AllenSDK/issues/660 and https://github.com/AllenInstitute/AllenSDK/issues/659 no longer use scipy.misc.imresize, which has been removed from scipy - https://github.com/AllenInstitute/AllenSDK/issues/661 miscellaneous fixes to example notebooks. Affected notebooks: - https://allensdk.readthedocs.io/en/latest/static/examples/nb/cellspecimenmapping.html - https://allensdk.readthedocs.io/en/latest/static/examples/nb/pulsestimulus.html - https://allensdk.readthedocs.io/en/latest/static/examples/nb/receptive_fields.html
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Published by NileGraddis about 7 years ago
https://github.com/alleninstitute/allensdk - Release 0.16.2
Added - https://github.com/AllenInstitute/AllenSDK/issues/549 Transforms for tissuecyte registration accessible from allensdk - https://github.com/AllenInstitute/AllenSDK/pull/568 Release instructions for future maintainers.
Changed - https://github.com/AllenInstitute/AllenSDK/issues/582 Documentation builds from a yml config in python 3.7
Bug Fixes - https://github.com/AllenInstitute/AllenSDK/issues/523 pip no longer fails on new conda environment because of tables
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Published by nicain about 7 years ago
https://github.com/alleninstitute/allensdk - Release 0.16.1
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Published by nicain over 7 years ago