AllenSDK Versions Save

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

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 manual_structure_acronym 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 left_right_ccf_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

• 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

• Major internal refactor to BehaviorSession, BehaviorOphysExperiment classes. Implements DataObject pattern for fetching and serialization of data.

Changes:

• Reorder Visual Behavior metadata columns to be more helpful

minor fix to cloud cache

Released 2021-08-11

• Added ability to specify a static cache directory (use_static_cache=True) to instantiate VisualBehaviorOphysProjectCache.from_local_cache()
• Added 'experience_level', 'passive' and 'image_set' columns to ophys_experiments_table
• Added 'ophys_cells_table' metadata table to track the relationship between ophys_experiment_id and cell_specimen_id