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Welcome to the cave-scripts wiki!

In the notebooks folder, there are several working scripts to interact with CaveClient.

Data

Examples

example_data.h5 and dash_example_data.h5 are from NeuroglancerAnnotationUI.

Nucleus

h01_cell_body_nucleus_matrix_may16_2023.csv is an original table that contains nucleus id, volume, position and bounding box's position. Daniel Berger compiled on May 16, 2023.

h01_nucleus_table_data.h5 is a table ingested into CAVE.

About Columns:

• id: ID in the VAST segmentation file (for neurons/glia this should be consistent with the 'dbid' value in other tables)
• volume: volume estimate of cell body or nucleus in cubic micrometers, at very low resolution (mip6 every 128th section for neurons/glia, mip7 every 16th section for bv nuclei, manually painted)
• pt_position: X, Y, Z anchor point within cell body or nucleus, in pixels at 8x8x33 nm
• bb_start_position: Xmin, Ymin, Zmin of bounding box of cell body or nucleus, in pixels at 8x8x33 nm
• bb_end_position: Xmax, Ymax, Zmax of bounding box of cell body or nucleus, in pixels at 8x8x33 nm

Annotations

dbcells-dump.csv contains annotations previously done for H01.

dbcells_dump_table_data.h5 is a table ingested into CAVE.

About Columns:

• pt_position: X, Y, Z anchor point within cell body or nucleus, in pixels at 8x8x33 nm
• classification_system: comma-seperated string joined from 'dbsubcelltype', 'dbsubcelltype2', and 'dbsubcelltype3'
• cell_type: cell type (manually classified)
  • 0: [U] unknown
  • 1: [P] pyramidal
  • 2: [I] interneuron
  • 3: [N] unclassified neuron
  • 4: [A] astrocyte
  • 5: [O] oligodendrocyte
  • 6: [G] mg/opc
  • 7: [C] 'c-shaped' cell (also mg/opc)
  • 8: [B] blood vessel cell (does not occur in this list)
  • 9: [S] Spiny stellate
  • 10: [E] Excitatory/spiny with atypical tree\n% Evelinas blood vessel nucleus types are
  • 11: 'Pericytes'
  • 12: 'vSMC'
  • 13: 'fibroblast'
  • 14: 'perivascular lymphocytes'
  • 15: 'perivascular macrophages'
  • 16: 'undecided' (unspecified blood vessel cell)
  • 17: 'Endothelial cells'
  • 18: 'circulating imm'

SNEMI

You can download SNEMI data in here