Background Components for Caiman

CHANGELOG.md

@@ -40,6 +40,7 @@
 * Manual construction of a `DatasetIOConfiguration` now requires the field `dataset_name`, and will be validated to match the final path of `location_in_file`. Usage via the automated constructors is unchanged. [PR #767](https://github.com/catalystneuro/neuroconv/pull/767)
 * Enhance `get_schema_from_method_signature` to extract descriptions from the method docval. [PR #771](https://github.com/catalystneuro/neuroconv/pull/771)
 * Avoid writing `channel_to_uV` and `offset_to_uV` in `add_electrodes`  [PR #803](https://github.com/catalystneuro/neuroconv/pull/803)
+* `BaseSegmentationExtractorInterface` now supports optional background plane segmentations and associated fluorescence traces [PR #783](https://github.com/catalystneuro/neuroconv/pull/783)
 
 
 # v0.4.7 (February 21, 2024)

src/neuroconv/datainterfaces/ophys/basesegmentationextractorinterface.py

@@ -113,6 +113,7 @@ def add_to_nwbfile(
         metadata: Optional[dict] = None,
         stub_test: bool = False,
         stub_frames: int = 100,
+        include_background_segmentation: bool = False,
         include_roi_centroids: bool = True,
         include_roi_acceptance: bool = True,
         mask_type: Optional[str] = "image",  # Literal["image", "pixel", "voxel"]
@@ -130,6 +131,9 @@ def add_to_nwbfile(
             The metadata for the interface
         stub_test : bool, default: False
         stub_frames : int, default: 100
+        include_background_segmentation : bool, default: False
+            Whether to include the background plane segmentation and fluorescence traces in the NWB file. If False,
+            neuropil traces are included in the main plane segmentation rather than the background plane segmentation.
         include_roi_centroids : bool, default: True
             Whether to include the ROI centroids on the PlaneSegmentation table.
             If there are a very large number of ROIs (such as in whole-brain recordings),
@@ -172,6 +176,7 @@ def add_to_nwbfile(
             segmentation_extractor=segmentation_extractor,
             nwbfile=nwbfile,
             metadata=metadata,
+            include_background_segmentation=include_background_segmentation,
             include_roi_centroids=include_roi_centroids,
             include_roi_acceptance=include_roi_acceptance,
             mask_type=mask_type,

src/neuroconv/tools/roiextractors/__init__.py

@@ -1,4 +1,6 @@
 from .roiextractors import (
+    add_background_fluorescence_traces,
+    add_background_plane_segmentation,
     add_devices,
     add_fluorescence_traces,
     add_image_segmentation,