Selecting ROIs for Conversion

By default, segmentation interfaces write all ROIs from the source data to the NWB file. In some cases, for example after curating the segmentation output, you may want to include only a subset of the ROIs in the source data. To support this, segmentation interfaces accept the roi_ids_to_add parameter in add_to_nwbfile() (and create_nwbfile()) to specify which ROIs to write.

Inspecting Available ROI IDs

Before filtering, you can inspect the available ROI IDs using the roi_ids property on any segmentation interface:

from neuroconv.tools.testing.mock_interfaces import MockSegmentationInterface

interface = MockSegmentationInterface(num_rois=20)

# Inspect all available ROI IDs
print("All ROI IDs:", interface.roi_ids)

Filtering ROIs During Conversion

Pass the roi_ids_to_add parameter to create_nwbfile() or add_to_nwbfile() to include only a subset of ROIs:

from neuroconv.tools.testing.mock_interfaces import MockSegmentationInterface

interface = MockSegmentationInterface(num_rois=20)

# Convert with only specific ROIs
nwbfile = interface.create_nwbfile(roi_ids_to_add=["roi_00", "roi_03", "roi_10"])

# Verify only selected ROIs are in the file
plane_segmentation = nwbfile.processing["ophys"]["ImageSegmentation"]["PlaneSegmentation"]
print("Number of ROIs in NWB:", len(plane_segmentation))  # 3