All notable changes to this project will be documented in this file.
- BrainObservatoryCache.get_ophys_experiment_events
- BrainObservatoryCache.get_ophys_experiments and get_experiment_containers accept reporter_lines argument
- BrainObservatoryCache.ge_ophys_experiment_analysis
- Cache subclasses can have their manifest locations set via environment variable
- bumped lower limit of pandas to 0.17, removed upper limit
- changed CellTypesCache cell data structure to be less nested, more flat. Requires update to manifest and re-download of cells.json.
- simplified MouseConnectivityCache data structure. Requires update to manifest and re-download of experiments.json.
- stopped using deprecated function in SimpleTree
- regression tests for Brain Observatory analysis
- Numerous Python 2/3 compatibility fixes
- Improved spike filtering in ephys.ephys_features
- CellTypesCache.get_cells has a new
speciesargument.
- MouseConnectivityCache downloads structure masks instead of computing them.
- ABS-64; Jupyterhub Dockerfiles
- PR #13; Manifest error check
ABS-132; changed to Allen Institute Software License ABS-129; StructureTree converts color hex triplet to 8-bit color triplet ABS-125; update expected data for unmocked tests PBS-358; update extract_trace module to deal with motion border case ABS-85; allow variable long square start time in ephys feature extractor
- BrainObservatoryNwbDataSet.get_demixed_traces
- BrainObservatoryNwbDataSet.get_pupil_location
- BrainObservatoryNwbDataSet.get_pupil_size
- BrainObservatoryApi.get_cell_specimen_id_mapping
- allensdk.brain_observatory.receptive_field_analysis
- allensdk.brain_observatory.demixer
- BrainObservatoryCache.get_ophys_experiments returns "acquisition_age_days" instead of "age_days". The new field describes the age of the animal on the day of experiment acquisition.
- BrainObservatoryCache.get_experiment_containers no longer returns "age_days".
- BrainObservatoryCache.get_ophys_experiments accepts a list of cell_specimen_ids for additional filtering
- json_utilities uses simplejson for better NaN handling
- issue #42: Caching behavior in MouseConnectivityCache for CCF volumes fixed
- GLIF examples, documentation fixed
- ReferenceSpace is a new class for relating structure graphs and annotation volumes.
- Standardized caching and paging decorators
- 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.
- 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.
- 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.
- 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: https://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.
- MouseConnectivityCache has a new constructor argument for specifying CCF version.
- Github issue #16 (jinja2 requirement)
- Github pull request #21 (spurious "i" typo) in r_neuropil.py
- neuropil subtraction algorithm (brain_observatory.r_neuropil) faster and more robust
- formatting changes for better PEP8 compliance
- preparation for Python 3 support
- updated Dockerfiles
- Github issue #17 (scipy requirement)
- 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.
- 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
- 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
- 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)
- MouseConnectivityCache.get_projection_matrix, method for building a signal matrix from injection structure to projection structure.
- CellTypesCache.get_morphology_features, method for retrieving morphology features for all cells
- CellTypesCache.get_all_features, method for retrieving both morphology and ephys features for all cells in a single table
- new RmaTemplate class enables construction of queries with jinja2 template library.
- Jupyter notebook examples added to documentation.
- Api.retrieve_parsed_json_over_http respects post parameter.
- improved installation of dependencies.
- Ontology.get_child_ids and Ontology.get_descendant_ids accept a list of ids instead of a variable length argument list.
- API Access/Data API Client documentation better reflects new 0.10.x allensdk.api.query modules.
- Cache.wrap method defaults to save_as_json=False.
- Cache.wrap method defaults to returning json rather than a pandas dataframe (new parameter return_dataframe=False).
- BiophysicalApi.cache_data throws an exception if no data is found for a neuronal model id.
- Replaced brainscales Dockerfile with neuralenseble Dockerfiles.
- MouseConnectivityCache.get_projection_matrix, method for building a signal matrix from injection structure to projection structure.
- CellTypesCache.get_morphology_features, method for retrieving morphology features for all cells
- CellTypesCache.get_all_features, method for retrieving both morphology and ephys features for all cells in a single table
- Ontology.get_child_ids and Ontology.get_descendant_ids accept a list of ids instead of a variable length argument list.
- Manifest and Cache classes for keeping track of files
- MouseConnectivityApi class for downloading data from the Mouse Connectivity Atlas
- MouseConnectivityCache fclass or keeping track of files
- CellTypesCache for keeping track of cell types files
- Ontology class for manipulating structures
- Rma class for formalizing API queries
- GridDataApi for downloading expression and projection grid volumes
- EphysFeatureExtractor module for computing ephys features used in Cell Types Database
- json_utilities has better numpy data type serialization support
- Documentation updated
- Installation/Makefile bug
- Everything: initial release!