Neuroconv

Back-compatibility break
* The `CEDRecordingInterface` has now been removed; use the `Spike2RecordingInterface` instead. [PR 602](https://github.com/catalystneuro/neuroconv/pull/602)

Features
* Added support for python 3.12 [PR 626](https://github.com/catalystneuro/neuroconv/pull/626)
* Added `session_start_time` extraction to `FicTracDataInterface`. [PR 598](https://github.com/catalystneuro/neuroconv/pull/598)
* Added `imaging_plane_name` keyword argument to `add_imaging_plane` function to determine which imaging plane to add from the metadata by name instead of `imaging_plane_index`.
* Added reference for `imaging_plane` to default plane segmentation metadata. [PR 594](https://github.com/catalystneuro/neuroconv/pull/594)
* Changed Compass container for Position container in the `FicTracDataInterface`. [PR 606](https://github.com/catalystneuro/neuroconv/pull/605)
* Added option to write units in meters by providing a radius in `FicTracDataInterface`. [PR 606](https://github.com/catalystneuro/neuroconv/pull/605)
* Added `parent_container` keyword argument to `add_photon_series` that defines whether to add the photon series to acquisition or 'ophys' processing module. [PR 587](https://github.com/catalystneuro/neuroconv/pull/587)
* Added Pydantic data models of `DatasetInfo` (immutable summary of core dataset values such as maximum shape and dtype) and `DatasetConfiguration` for both HDF5 and Zarr datasets (the optional layer that specifies chunk/buffering/compression). [PR 567](https://github.com/catalystneuro/neuroconv/pull/567)
* Added alignment methods to `FicTracDataInterface`. [PR 607](https://github.com/catalystneuro/neuroconv/pull/607)
* Added alignment methods support to `MockRecordingInterface` [PR 611](https://github.com/catalystneuro/neuroconv/pull/611)
* Added `NeuralynxNvtInterface`, which can read position tracking NVT files. [PR 580](https://github.com/catalystneuro/neuroconv/pull/580)
* Adding radius as a conversion factor in `FicTracDataInterface`. [PR 619](https://github.com/catalystneuro/neuroconv/pull/619)
* Coerce `FicTracDataInterface` original timestamps to start from 0. [PR 619](https://github.com/catalystneuro/neuroconv/pull/619)
* Added configuration metadata to `FicTracDataInterface`. [PR 618](https://github.com/catalystneuro/neuroconv/pull/618)
* Expose number of jobs to `automatic_dandi_upload`. [PR 624](https://github.com/catalystneuro/neuroconv/pull/624)
* Added `plane_segmentation_name` keyword argument to determine which plane segmentation to add from the metadata by name instead of `plane_segmentation_index`.
`plane_segmentation_name` is exposed at `BaseSegmentationExtractorInterface.add_to_nwbfile()` function to support adding segmentation output from multiple planes. [PR 623](https://github.com/catalystneuro/neuroconv/pull/623)
* Added `SegmentationImages` to metadata_schema in `BaseSegmentationExtractorInterface` to allow for the modification of the name and description of Images container and description of the summary images. [PR 622](https://github.com/catalystneuro/neuroconv/pull/622)
* Default chunking pattern of RecordingInterfaces now attempts to use as many channels as possible up to 64 total, and fill with as much time as possible up to the `chunk_mb`. This also required raising the lower HDMF version to 3.11.0 (which introduced 10 MB default chunk sizes). [PR 630](https://github.com/catalystneuro/neuroconv/pull/630)

Fixes
* Remove `starting_time` reset to default value (0.0) when adding the rate and updating the `photon_series_kwargs` or `roi_response_series_kwargs`, in `add_photon_series` or `add_fluorescence_traces`. [PR 595](https://github.com/catalystneuro/neuroconv/pull/595)
* Changed the date parsing in `OpenEphysLegacyRecordingInterface` to `datetime.strptime` with the expected date format explicitly set to `"%d-%b-%Y %H%M%S"`. [PR 577](https://github.com/catalystneuro/neuroconv/pull/577)
* Pin lower bound HDMF version to `3.10.0`. [PR 586](https://github.com/catalystneuro/neuroconv/pull/586)

Deprecation
* Removed `use_times` and `buffer_size` from `add_photon_series`. [PR 600](https://github.com/catalystneuro/neuroconv/pull/600)

Testing
* Adds `MockImagingInterface` as a general testing mechanism for ophys imaging interfaces [PR 604](https://github.com/catalystneuro/neuroconv/pull/604).

Features

* `DeepLabCutInterface` now allows using custom timestamps via `set_aligned_timestamps` method before running conversion. [PR 531](https://github.com/catalystneuro/neuroconv/pull/532)

Fixes

* Reorganize timeintervals schema to reside in `schemas/` dir to ensure its inclusion in package build. [PR 573](https://github.com/catalystneuro/neuroconv/pull/573)

Fixes

* The `sonpy` package for the Spike2 interface no longer attempts installation on M1 Macs. [PR 563](https://github.com/catalystneuro/neuroconv/pull/563)
* Fixed `subset_sorting` to explicitly cast `end_frame` to int to avoid SpikeInterface frame slicing edge case. [PR 565](https://github.com/catalystneuro/neuroconv/pull/565)

Fixes

* Exposed `es_key` argument to users where it was previously omitted on `MaxOneRecordingInterface`, `OpenEphysLegacyRecordingInterface`, and `OpenEphysRecordingInterface`. [PR 542](https://github.com/catalystneuro/neuroconv/pull/542)
* Added deepcopy for metadata in `make_nwbfile_from_metadata`. [PR 545](https://github.com/catalystneuro/neuroconv/pull/545)
* Fixed edge case in `subset_sorting` where `end_frame` could exceed recording length. [PR 551](https://github.com/catalystneuro/neuroconv/pull/551)
* Alter `add_electrodes` behavior, no error is thrown if a property is present in the metadata but not in the recording extractors. This allows the combination of recording objects that have different properties. [PR 558](https://github.com/catalystneuro/neuroconv/pull/558)

Features

* Added converters for Bruker TIF format to support multiple streams of imaging data.
Added `BrukerTiffSinglePlaneConverter` for single plane imaging data which initializes a `BrukerTiffSinglePlaneImagingInterface` for each data stream.
The available data streams can be checked by `BrukerTiffSinglePlaneImagingInterface.get_streams(folder_path)` method.
Added `BrukerTiffMultiPlaneConverter` for volumetric imaging data with `plane_separation_type` argument that defines
whether to load the imaging planes as a volume (`"contiguous"`) or separately (`"disjoint"`).
The available data streams for the defined `plane_separation_type` can be checked by `BrukerTiffMultiPlaneImagingInterface.get_streams(folder_path, plane_separation_type)` method.
* Added FicTrac data interface. [PR 517](https://github.com/catalystneuro/neuroconv/pull/#517)

Documentation and tutorial enhancements

* Added FicTrac to the conversion gallery and docs API. [PR 560](https://github.com/catalystneuro/neuroconv/pull/#560)

Fixes

* Propagated additional arguments, such as `cell_id`, from the `metadata["Icephys"]["Electrodes"]` dictionary used in `tools.neo.add_icephys_electrode`. [PR 538](https://github.com/catalystneuro/neuroconv/pull/538)
* Fixed mismatch between expected `Electrodes` key in `tools.neo.add_icephys_electrode` and the metadata automatically generated by the `AbfInterface`. [PR 538](https://github.com/catalystneuro/neuroconv/pull/538)

Back-compatibility break

* Create separate `.add_to_nwbfile` method for all DataInterfaces. This is effectively the previous `.run_conversion` method but limited to operations on an in-memory `nwbfile`: pynwb.NWBFile` object and does not handle any I/O. [PR 455](https://github.com/catalystneuro/neuroconv/pull/455)

Fixes

* Set gzip compression by default on spikeinterface based interfaces `run_conversion`. [PR 499](https://github.com/catalystneuro/neuroconv/pull/#499)

* Temporarily disabled filtering for all-zero traces in `add_fluorescence_traces` as the current implementation is very slow for nearly all zero traces (e.g. suite2p deconvolved traces). [PR 527](https://github.com/catalystneuro/neuroconv/pull/527)

Features

* Added stream control with the `stream_name` argument to the `NeuralynxRecordingExtractor`. [PR 369](https://github.com/catalystneuro/neuroconv/pull/369)

* Added a common `.temporally_align_data_interfaces` method to the `NWBConverter` class to use as a specification of the protocol for temporally aligning the data interfaces of the converter. [PR 362](https://github.com/catalystneuro/neuroconv/pull/362)

* Added `CellExplorerRecordingInterface` for adding data raw and lfp data from the CellExplorer format. CellExplorer's new format contains a `basename.session.mat` file containing
rich metadata about the session which can be used to extract the recording information such as sampling frequency and type and channel metadata such as
groups, location and brain area [488](https://github.com/catalystneuro/neuroconv/pull/488)

* `CellExplorerSortingInterface` now supports extracting sampling frequency from the new data format. CellExplorer's new format contains a `basename.session.mat` file containing
rich metadata including the sorting sampling frequency [PR 491](https://github.com/catalystneuro/neuroconv/pull/491) and [PR #502](https://github.com/catalystneuro/neuroconv/pull/502)
* Added `MiniscopeBehaviorInterface` for Miniscope behavioral data. The interface uses `ndx-miniscope` extension to add a `Miniscope` device with the behavioral camera metadata,
and an `ImageSeries` in external mode that is linked to the device. [PR 482](https://github.com/catalystneuro/neuroconv/pull/482)
* `CellExplorerSortingInterface` now supports adding channel metadata to the nwbfile with `write_ecephys_metadata=True` as a conversion option [PR 494](https://github.com/catalystneuro/neuroconv/pull/494)

* Added `MiniscopeImagingInterface` for Miniscope imaging data stream. The interface uses `ndx-miniscope` extension to add a `Miniscope` device with the microscope device metadata,
and the imaging data as `OnePhotonSeries`. [PR 468](https://github.com/catalystneuro/neuroconv/pull/468)

* Added `MiniscopeConverter` for combining the conversion of Miniscope imaging and behavioral data streams. [PR 498](https://github.com/catalystneuro/neuroconv/pull/498)

Improvements

* Avoid redundant timestamp creation in `add_eletrical_series` for recording objects without time vector. [PR 495](https://github.com/catalystneuro/neuroconv/pull/495)

* Avoid modifying the passed `metadata` structure via `deep_dict_update` in `make_nwbfile_from_metadata`. [PR 476](https://github.com/catalystneuro/neuroconv/pull/476)

Testing

* Added gin test for `CellExplorerRecordingInterface`. CellExplorer's new format contains a `basename.session.mat` file containing
rich metadata about the session which can be used to extract the recording information such as sampling frequency and type and channel metadata such as
groups, location and brain area [488](https://github.com/catalystneuro/neuroconv/pull/488).
* Added gin test for `CellExplorerSortingInterface`. CellExplorer's new format contains a `basename.session.mat` file containing
rich metadata about the session which can be used to extract the recording information such as sampling frequency and type and channel metadata such as
groups, location and brain area [PR 494](https://github.com/catalystneuro/neuroconv/pull/494).