Release Notes (0.14.5)

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.