AllenInstitute/AllenSDK

View on GitHub

code for reading and processing Allen Institute for Brain Science data

Stars: 398
Forks: 163
Open beginner issues: 0
Indexed issues: 377

Dominant language: Jupyter Notebook
License: No license data
Last GitHub push: Jul 6, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue help wanted
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

377 open issues indexed

[Bug]: multipletests import fails in receptive_field.py Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 92/100

AllenInstitute/AllenSDK#2783 · Opened Sep 14, 2026
[Bug]: Allensdk running on paper space is stuck in an infinite loading loop for sessions Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2782 · 1 comment · Opened Aug 28, 2026
Visual coding dataset channels.y==channels.z in persession nwb file? Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2776 · Opened Mar 13, 2026
on-prem test is out of date and cannot pass Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2773 · Opened Feb 17, 2026
Tro Open

bug

Difficulty 5/5 Over a week Newbie friendliness 5/100

AllenInstitute/AllenSDK#2766 · Opened Nov 27, 2025
Spike waveform templates in the allensdk? Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

AllenInstitute/AllenSDK#2763 · Opened Nov 19, 2025
Update on feature updates Open

question

Difficulty 5/5 Over a week Newbie friendliness 20/100

AllenInstitute/AllenSDK#2761 · 3 comments · 4 reactions · Opened Jun 12, 2025
Spinal Cord ccf Open

question

Difficulty 5/5 Over a week Newbie friendliness 20/100

AllenInstitute/AllenSDK#2760 · Opened May 16, 2025
documentation format availability? Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

AllenInstitute/AllenSDK#2759 · Opened May 15, 2025
map from natural scene template ID to stimulus condition ID for brain observatory datasets? Open

question

Difficulty 3/5 1-2 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2758 · Opened Apr 6, 2025
Assistance with Accessing Expression Grid Data via Allen Brain Atlas API Open

question

Difficulty 5/5 Over a week Newbie friendliness 20/100

AllenInstitute/AllenSDK#2755 · Opened Mar 14, 2025
Some metadata csv files don't get downloaded from `EcephysProjectCachce.from_warehouse` Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

AllenInstitute/AllenSDK#2753 · 6 comments · Opened Dec 13, 2024
Add progress bar when loading data Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

AllenInstitute/AllenSDK#2752 · Opened Nov 24, 2024
Missing links to model example .tgz files Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

AllenInstitute/AllenSDK#2749 · Opened Sep 9, 2024
automatic retrival of connections data Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

AllenInstitute/AllenSDK#2748 · Opened Sep 9, 2024
incorrect values for `imaging_depth` column in VisualBehaviorOphysProjectCache ophys_experiment_table Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2745 · 2 comments · Opened Aug 3, 2024
Retrieving Shuffled Frame IDs Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

AllenInstitute/AllenSDK#2743 · Opened Apr 7, 2024
Unable to download cache files Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2742 · Opened Jan 16, 2024
Creating drifting gratings (frame by frame) Open

question

Difficulty 3/5 1-2 days Newbie friendliness 25/100

AllenInstitute/AllenSDK#2739 · Opened Dec 27, 2023
Broken .get_performance_metrics() method in VisualBehaviorNeuropixelsProjectCache.from_s3_cache(cache_dir=neuropixel_dataset_behavior) Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

AllenInstitute/AllenSDK#2733 · 2 comments · Opened Nov 9, 2023
Update conda-forge package Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 38/100

AllenInstitute/AllenSDK#2727 · 2 comments · Opened Oct 7, 2023
DriftingGratings.get_response() does not explain what the ncells+1'th response corresponds to Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

AllenInstitute/AllenSDK#2719 · Opened Aug 29, 2023
incorrect task parameter value in session metadata for TRAINING_0 and TRAINING_1 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2717 · 1 comment · Opened Aug 19, 2023
Simultaneously importing `ecephys_project_cache` and `behavior_ecephys_session` breaks nwb file reading Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2713 · 3 comments · Opened Aug 9, 2023
KeyError: 'sweeps_by_type' Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2711 · Opened Aug 4, 2023
How to access Neuropixels session end time? Open

question

Difficulty 3/5 1-2 days Newbie friendliness 25/100

AllenInstitute/AllenSDK#2709 · Opened Jul 27, 2023
Issue with statsmodels in allensdk install Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 30/100

AllenInstitute/AllenSDK#2705 · 1 comment · Opened Jul 23, 2023
how can I get the brain surface dorsal-ventral ccf coordinates for different probes? Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

AllenInstitute/AllenSDK#2702 · Opened Jul 19, 2023
Add 'quality' column to VBN units metadata table Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

AllenInstitute/AllenSDK#2696 · 1 comment · Opened Jul 12, 2023
Request (Allen Brain Observatory Data): Access to ophys metadata as csv files Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

AllenInstitute/AllenSDK#2694 · Opened Jul 2, 2023
Error reading NWB file while session cache is instantiated in workspace Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

AllenInstitute/AllenSDK#2693 · Opened Jun 26, 2023
JSONDecodeError when running oapi.get_structures_with_sets([1]) Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2684 · 1 comment · Opened May 25, 2023
Ophys NWB Conversion fails if a dff file is missing Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

AllenInstitute/AllenSDK#2683 · 9 comments · Opened May 9, 2023
add_lfp_to_nwb Function seems to add the LFP probe data twice Open

question

Difficulty 3/5 1-2 days Newbie friendliness 42/100

AllenInstitute/AllenSDK#2681 · Opened Apr 26, 2023
Optogenetic information in NWB files could be using a more specific data type Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

AllenInstitute/AllenSDK#2680 · Opened Apr 26, 2023
datasets diffrences Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

AllenInstitute/AllenSDK#2677 · 1 comment · Opened Apr 13, 2023
extract event trace Open

question

Difficulty 4/5 3-5 days Newbie friendliness 20/100

AllenInstitute/AllenSDK#2676 · Opened Apr 13, 2023
Using imread for Ophys Projections automatically casts them to floats Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

AllenInstitute/AllenSDK#2672 · Opened Mar 31, 2023
Flipped running polarity for VBN behavior only sessions Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 32/100

AllenInstitute/AllenSDK#2661 · 13 comments · Opened Feb 16, 2023
Backward compatibility between allensdk 2.13.5 and 2.14.1 broken for VBN manifest 0.3.0 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 42/100

AllenInstitute/AllenSDK#2646 · Opened Jan 18, 2023
Add is_sham_change to VBN stimulus_presentations table Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

AllenInstitute/AllenSDK#2643 · 2 comments · Opened Jan 12, 2023
VBN NWB files need to be updated to reflect LFP data release Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

AllenInstitute/AllenSDK#2641 · Opened Jan 12, 2023
Notebooks should use seeds Open

enhancement notebook

Difficulty 3/5 1-2 days Newbie friendliness 45/100

AllenInstitute/AllenSDK#2636 · Opened Dec 14, 2022
Inconsistent datasets from `EcephysSession.presentationwise_spike_times method` Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

AllenInstitute/AllenSDK#2634 · 1 comment · Opened Dec 13, 2022
Revert optional traces logic once VBO updated data released Open

vbo

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

AllenInstitute/AllenSDK#2632 · 1 comment · Opened Dec 12, 2022
Progress bar for Visual Coding Neuropixel csv files downloading Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 48/100

AllenInstitute/AllenSDK#2631 · Opened Dec 10, 2022
Unskip tests Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

AllenInstitute/AllenSDK#2628 · Opened Dec 8, 2022
Move eyetracking into a github repo Open

Epic

Difficulty 5/5 Over a week Newbie friendliness 25/100

AllenInstitute/AllenSDK#2621 · 1 comment · Opened Nov 30, 2022
Package add on Eye Tracking data for Saskia. Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

AllenInstitute/AllenSDK#2608 · 2 comments · Opened Nov 15, 2022
Remove `from_json` functionality. Open

AllenInstitute/AllenSDK#2607 · 2 comments · 1 assignee · Opened Nov 15, 2022

AllenInstitute/AllenSDK

Get new issues in your inbox