Release Notes (0.14.5)

David Feng edited this page Jul 27, 2018 · 5 revisions

The 0.14.5 release coincides with the release of additional mouse electrophysiology and morphology data in the Allen Cell Types Database. We have simplified the data structure returned by get_cells() to be more flat, so you will be prompted to update your manifest. To use the simpler format and access the new data, remove the following files:

  • CellTypesCache() manifest.json
  • cells.json
  • ephys_features.csv
  • morphology_features.csv

Specifically, you'll see that the cell dictionaries returned by get_cells() that have the following flat list of fields:

  • reporter_status: positive / negative (formerly: cre reporter positive, cre reporter negative)
  • cell_soma_location: now an array of [x,y,z] coordinates
  • species: formerly inside of the "donor" sub-dictionary
  • id: database ID of the cell
  • name: more human readable identifier of the cell
  • structure_layer_name: formerly inside of "cortex_layer" sub-dictionary
  • structure_area_id: non-layer-specific brain area (for mouse cells, this used to be the layer-specific structure record)
  • structure_area_abbrev: abbreviation of brain area name
  • transgenic_line: transgenic line name of the mouse (N/A for human cells)
  • dendrite_type: spiny / aspiny / sparsely spiny
  • apical: apical dendrite completeness in the slice - intact / 'NA'
  • reconstruction_type: None / full / dendrite-only
  • disease_state: None / epilepsy / tumor
  • donor_id: unique ID of the donor
  • structure_hemisphere: hemisphere from which the sample was taken
  • normalized_depth: relative position [0,1] between pia and white matter in the cortex

We have also simplified the data structure returned by MouseConnectivityCache.get_experiments(), so you will be prompted to update your connectivity manifest. To use the simpler format and access the new data, remove the following files:

  • MouseConnectivityCache() manifest.json
  • experiments.json

Specifically, get_experiments will now return a list of dictionaries with the following fields:

  • gender: M / F
  • injection_structures: list of structure IDs
  • injection_volume: volume of the injection site in um^3
  • injection_x, injection_y, injection_z: 3D coordinates inside of injection site
  • specimen_name: more human readable identifier of the data set
  • strain: mouse strain
  • structure_id: ID of primary injection structure
  • structure_name: full name of primary injection structure
  • transgenic_line: name of mouse transgenic line
  • transgenic_line_id: ID of transgenic line
  • id: ID of data set

Additional changes:

  • increased pandas minimum version to 0.17, removed the upper limit
  • added regression tests to the Brain Observatory analysis modules to ensure py3/py2 numerical compatibility.
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