eulerlab/eyewire2-data

Eyewire II - Resource paper - Data

Data accompanying the Eyewire II resource paper. Consumed by eyewire2-functional-analysis and eyewire2-figures — see those repos' READMEs for how to download and place this data.

Contents

• data-2p/ — preprocessed 2P calcium-imaging data (5 recording fields), stored as parquet files. See data-2p/README.md.
  • smh/ — raw ScanM stimulus header files, one per recording field/stimulus.
  • stimuli/ — QDSpy stimulator scripts and stimulus descriptions (chirp, moving bar, mouse-cam movies). See data-2p/stimuli/README.md.
• data-em/
  • dataframes/ — EM-derived analysis dataframes.
    • df_all_neurons_*.parquet — dataframe holding cell information
    • df_ribbons_*.parquet — dataframe holding ribbon information
    • fig8_df_rbc_celltype_*.parquet — dataframe for figure 8
    • fig8_df_rbc_synapse_*.parquet — dataframe for figure 8
  • misc/
    • Movie_tissue-and-overview-supplemental-1.mp4 — Movie of EM stack
• images/
  • highres-images-2p/ — GCL0.tif … GCL4.tif. high-res versions of the five 2P recording fields
  • em-fields/ — images in EM of the five 2P fields
• spreadsheets/ — master proofreading spreadsheets maintained in eyewire2-master-sheet-cleanup:
  • Eyewire II Proofread Cells Main List - All Cells {date}.csv — the cell list (WIP)
  • Eyewire II Proofread Cells Main List - All BCs {date}.csv — the current bipolar-cell list (WIP)
  • Eyewire II Proofread Cells Main List - All Glia {date}.csv — the glia list (WIP)
  • Eyewire II Proofread Cells Main List - EM-2p-mapping {date}.csv — known EM-cell ↔ 2P-ROI correspondences, used to fit the 2P-to-EM coordinate registration
  • Eyewire II Proofread Cells Main List - Cell types and properties {date}.csv — current cell type description (WIP)
• swc/, swc.zip, swc-examples.zip — EM neuron skeletons in SWC format. swc.zip contains skeletons for all cells used in the paper (optional download); swc-examples.zip contains just the subset shown in the figures. swc/ itself isn't committed (see .gitignore) — unzip one of the archives into it locally.
• track_proofreading/, track_proofreading.zip — per-cell proofreading changelogs (changelogs_csv/segid_changelog_df_<segid>_<name>.csv), one CSV per segment ID recording its proofreading edit history. Like swc/, only the zipped version is committed.