Allensdk

Added

- ReferenceSpace is a new class for relating structure graphs and annotation volumes.
- Standardized caching and paging decorators

Changed

- Ontology has been deprecated in favor of StructureTree.
- MouseConnectivityCache uses StructureTree internally (ontology-based methods are deprecated)
- CellTypesCache and MouseConnectivityCache use cacher decorator
- GlifApi has stateless methods now. Old methods are deprecated.

Fixed

- Github issue 35 - MouseConnectivityCache's manifest now uses CCF-version- and resolution-specific file names for masks. The masks now live inside the CCF version directory. Users must download a new manifest.

Fixed

- Github issues 23, 28 - added a new dependency "requests_toolbelt" and upgraded API database for more reliable large file downloads.
- Github issue 26 - better documentation for structure unionize records.
- Github issue 25 - documentation errors in brain observatory analysis.

Changed

- New CCF annotation volume with complete cortical areas and layers.
- Mouse Connectivity structure unionize records have been computed for new CCF. Previous records are available here: http://download.alleninstitute.org/informatics-archive/june-2016/mouse_projection/
- Github issue 27 - MouseConnectivityCache.get_structure_unionizes returns only requested structures, not all descendants. Added a separate argument for descendant inclusion.

Added

- MouseConnectivityCache has a new constructor argument for specifying CCF version.

Fixed

- Github issue 16 (jinja2 requirement)
- Github pull request 21 (spurious "i" typo) in r_neuropil.py

Changed

- neuropil subtraction algorithm (brain_observatory.r_neuropil) faster and more robust
- formatting changes for better PEP8 compliance
- preparation for Python 3 support
- updated Dockerfiles

Fixed

- Github issue 17 (scipy requirement)

Added

- Support for the Allen Brain Observatory data (BrainObservatoryCache and BrainObservatoryApi classes).
- Code for neurpil subtraction, dF/F estimation, and tuning analysis.
- New ephys feature extractor (ephys_features.py, ephys_extractor.py). The old one is still there (feature_extractor.py) but should be considered deprecated.

Added

- CellTypesCache.get_cells has a new argument 'reporter_status', which accepts one or more ReporterStatus values.
- CellTypesApi.save_reconstruction_marker and CellTypesCache.get_reconstruction_marker download and open files containing positions that mark special points in reconstruction (truncation, early termination of reconstruction, etc).
- swc.read_marker_file for reading in marker files
- Morphology has new methods for manipulating the morphology tree structure
- allensdk.model.biophysical package supports active and passive models

Changed

- Morphology compartments are now Compartment objects that behave like dictionaries
- Compartment.children stores references to immediate descendant Compartments
- spike times in NWB files are stored in "analysis/spike_times" instead of "analysis/aibs_spike_times"
- NwbDataSet looks for spike times in both locations ("spike_times" first)
- glif_neuron_methods.py function names have been changed to be more standardized
- allensdk.model.biophysical_perisomatic package renamed to allensdk.model.biophysical
- NEURON dependency updated to 7.4 release 1370

Fixed

- MouseConnectivityCache.get_structure_mask bug fixed (github issue 8)
- CellTypesApi.get_ephys_sweeps returns sweeps in sweep number order (github issue 11)
- NwbDataSet.set_spike_times added maxshape(None,) to create_dataset (github issue 7)