AllenInstitute

Issues somebody may already be working on are listed last. List everything by date

• ETL non-Allen CONNECTS dataset

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  etl

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

  AllenInstitute/ConnectsCommonConnectivity#86 · Opened Oct 30, 2026

• Discussions with scientists about aligned morphology features

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  question

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

  AllenInstitute/ConnectsCommonConnectivity#85 · Opened Oct 30, 2026

• add missing documentation to `write_utils`

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

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

  AllenInstitute/ConnectsCommonConnectivity#84 · Opened Oct 30, 2026

• `validate_for_write` validates a copy but returns the originals

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  enhancement io

  Difficulty 2/5 1-3 hours Newbie friendliness 65/100

  AllenInstitute/ConnectsCommonConnectivity#83 · Opened Oct 30, 2026

• Write-time rules are split between writers.py and validation

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  enhancement io

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

  AllenInstitute/ConnectsCommonConnectivity#82 · Opened Oct 30, 2026

• `write_models` does not check cross-table references

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 4/5 3-5 days Newbie friendliness 48/100

  AllenInstitute/ConnectsCommonConnectivity#81 · Opened Oct 30, 2026

• `cell_cell_schema.yaml` redefines `dataitem_id`, dropping `range: DataItem` and adding a projection-specific description

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  bug documentation schema

  Difficulty 2/5 1-3 hours Newbie friendliness 68/100

  AllenInstitute/ConnectsCommonConnectivity#80 · Opened Oct 30, 2026

• Brain Region colors, readers. plotters

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  enhancement etl

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

  AllenInstitute/ConnectsCommonConnectivity#79 · Opened Oct 30, 2026

• Validate that referenced DataItems are registered when writing

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  bug io

  Difficulty 4/5 3-5 days Newbie friendliness 55/100

  AllenInstitute/ConnectsCommonConnectivity#78 · Opened Oct 30, 2026

• ETL tests & Data changelogs

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  documentation etl

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

  AllenInstitute/ConnectsCommonConnectivity#77 · 1 comment · Opened Oct 30, 2026

• give default 2D view to embedding space as well

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  enhancement schema

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

  AllenInstitute/ConnectsCommonConnectivity#76 · Opened Oct 30, 2026

• v111 spatial units in nm --> too large numbers for data type store as microns

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  etl

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

  AllenInstitute/ConnectsCommonConnectivity#75 · Opened Oct 30, 2026

• Merge ClusterMembership and CellToClusterMapping into one schema with an assignment-kind flag

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  enhancement io schema

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

  AllenInstitute/ConnectsCommonConnectivity#74 · Opened Oct 30, 2026

• io reader: derive region × region tables from item-level data

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  io

  Difficulty 5/5 Over a week Newbie friendliness 35/100

  AllenInstitute/ConnectsCommonConnectivity#73 · Opened Oct 30, 2026

• Add a direction slot to ProjectionMeasurementMatrix

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  bug schema

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

  AllenInstitute/ConnectsCommonConnectivity#72 · Opened Oct 30, 2026

• Add a DataItemType enum to record what a DataItem represents

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  bug schema

  Difficulty 5/5 Over a week Newbie friendliness 35/100

  AllenInstitute/ConnectsCommonConnectivity#71 · Opened Oct 30, 2026

• CCF validation

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  io schema

  Difficulty 5/5 Over a week Newbie friendliness 30/100

  AllenInstitute/ConnectsCommonConnectivity#70 · Opened Oct 30, 2026

• Avoid updating dashboard data for every open databrowser

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  Analysis Functions Dashboard bug Optimization

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

  AllenInstitute/MIES#2831 · Opened Oct 30, 2026

  Maintainers usually reply within 1 day

• CCF v1/2 clarity

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 5/5 Over a week Newbie friendliness 35/100

  AllenInstitute/atlas-assets#69 · Opened Oct 29, 2026

• CCF asset metadata fixes

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

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

  AllenInstitute/atlas-assets#68 · 2 comments · Opened Oct 29, 2026

• Register ccm data package to open data registry

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  documentation

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

  AllenInstitute/ConnectsCommonConnectivity#69 · Opened Oct 27, 2026

• Populate read_plot examples

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  documentation

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

  AllenInstitute/ConnectsCommonConnectivity#68 · Opened Oct 27, 2026

• ETL CCF coordinates for pathcseq and EM datasets

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  etl

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

  AllenInstitute/ConnectsCommonConnectivity#67 · Opened Oct 27, 2026

• Filtering by one value hides a file's other folders (multi-value annotations)

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  UX

  Difficulty 4/5 3-5 days Newbie friendliness 22/100

  AllenInstitute/biofile-finder#1015 · Opened Oct 27, 2026

  Maintainers usually reply within 1 day

• Compilation test does not catch code that breaks with DisableThreadsafeSupport()

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  bug PureEngineering

  Difficulty 2/5 1-3 hours Newbie friendliness 78/100

  AllenInstitute/MIES#2814 · 1 comment · Opened Oct 23, 2026

  Maintainers usually reply within 1 day

• Define how to represent parent and child clusters with the same name

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  io schema

  Difficulty 5/5 Over a week Newbie friendliness 35/100

  AllenInstitute/ConnectsCommonConnectivity#62 · Opened Oct 20, 2026

• Add graded QC to raw projection measurements

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  enhancement schema

  Difficulty 4/5 3-5 days Newbie friendliness 48/100

  AllenInstitute/ConnectsCommonConnectivity#61 · Opened Oct 20, 2026

• Cluster.level measures depth from the root; HierarchyCategory.level orders detail from leaves upward.

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  bug schema

  Difficulty 4/5 1-2 days Newbie friendliness 45/100

  AllenInstitute/ConnectsCommonConnectivity#60 · Opened Oct 20, 2026

• Encoding model: running/LP/pupil regressor issues found during methods verification

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

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

  AllenInstitute/npc_sessions#187 · Opened Oct 20, 2026

• Video-processing capsule code not public / provenance gaps (LP, Facemap, GammaEncoding)

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 4/5 3-5 days Newbie friendliness 28/100

  AllenInstitute/npc_sessions#186 · Opened Oct 20, 2026

• Digital encoder reads lag real time (serial backlog?) — running speed delayed by seconds

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 4/5 3-5 days Newbie friendliness 30/100

  AllenInstitute/npc_sessions#185 · Opened Oct 20, 2026

• lowpass_filter zero-fills NaN encoder reads before filtering

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

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

  AllenInstitute/npc_sessions#184 · Opened Oct 20, 2026

• Running speed timestamps are one frame (16.7 ms) late

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

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

  AllenInstitute/npc_sessions#183 · Opened Oct 20, 2026

• Running speed: non-physiological values up to 1e11 cm/s outside task (encoder read skips)

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

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

  AllenInstitute/npc_sessions#182 · Opened Oct 20, 2026

• Encoding model: running/LP/pupil regressor issues found during methods verification

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 4/5 3-5 days Newbie friendliness 48/100

  AllenInstitute/dynamic_routing_analysis#5 · Opened Oct 20, 2026

• No running speed in 22 SpontaneousRewards epochs (11 sessions, Aug–Sep 2023)

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 2/5 1-3 hours Newbie friendliness 68/100

  AllenInstitute/npc_sessions#181 · Opened Oct 20, 2026

• Lightning Pose models not trained or validated on DR video (label DR test set)

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 4/5 3-5 days Newbie friendliness 48/100

  AllenInstitute/npc_sessions#180 · Opened Oct 20, 2026

• Video-processing capsule code not public / provenance gaps (LP, Facemap, GammaEncoding)

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

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

  AllenInstitute/npc_lims#29 · Opened Oct 20, 2026

• NWB metadata errors: LP feature count, eye_tracking column descriptions, facemap unit/ROI

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 4/5 3-5 days Newbie friendliness 43/100

  AllenInstitute/npc_sessions#179 · Opened Oct 20, 2026

• lowpass_filter zero-fills NaN encoder reads before filtering

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 2/5 1-3 hours Newbie friendliness 58/100

  AllenInstitute/npc_stim#4 · Opened Oct 20, 2026

• Running speed: non-physiological values up to 1e11 cm/s outside task (encoder read skips)

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 3/5 1-2 days Newbie friendliness 56/100

  AllenInstitute/npc_stim#2 · Opened Oct 20, 2026

• Running speed delayed 0.1–3.1 s in 8 task sessions (and ~5–6 s in optotagging): add QC flag

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 4/5 3-5 days Newbie friendliness 52/100

  AllenInstitute/npc_sessions#178 · Opened Oct 20, 2026

• Run MVRDataset.validate() / add video-timing QC flag during NWB generation

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 4/5 3-5 days Newbie friendliness 46/100

  AllenInstitute/npc_sessions#177 · Opened Oct 20, 2026

• Video frame times wrong by up to 23 s in 5 sessions (unreported MVR lost frames)

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 4/5 3-5 days Newbie friendliness 52/100

  AllenInstitute/npc_sessions#176 · Opened Oct 20, 2026

• Add true DAG support to the clustering schema

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  bug schema

  Difficulty 1/5 Under an hour Newbie friendliness 68/100

  AllenInstitute/ConnectsCommonConnectivity#59 · Opened Oct 19, 2026

• Processing.__add__ turns parallel branches into a serial chain

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 5/5 Over a week Newbie friendliness 38/100

  AllenInstitute/biodata-schema#116 · Opened Oct 16, 2026

  Maintainers usually reply within 2 days

• link to HOMBA annotator app

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

  Difficulty 1/5 Under an hour Newbie friendliness 50/100

  AllenInstitute/HMBA_WB_Atlas#51 · Opened Oct 15, 2026

• Upgrade FluentUI v8 -> v9

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  dependencies

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

  AllenInstitute/biofile-finder#1004 · Opened Oct 14, 2026

  Maintainers usually reply within 1 day

• Integrate ambient RNA removal into the core upstream preprocessing pipeline

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel

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

  AllenInstitute/HMBA_WB_Atlas#50 · Opened Oct 14, 2026

• A user passable flag for which spatial/embedding spaces/views/plots should be viewed by default in Connectivity Viewer

  Open

  ⋯Report a problem with this issue

  • Is something wrong?

  • Already taken
  • Not beginner-friendly
  • Stale or invalid
  • Something else…
  • Send Cancel
  schema

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

  AllenInstitute/ConnectsCommonConnectivity#57 · 1 comment · Opened Oct 13, 2026