Extract roi indices from redcell.npy in Suite2pExtractor (#270)

* extract roi indices from redcell.npy * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Cody Baker <[email protected]>
catalystneuro · Jan 5, 2024 · bd18e5b · bd18e5b
1 parent c1e44ff
commit bd18e5b
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py b/src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py
@@ -166,7 +166,12 @@ def __init__(
             self._load_npy(file_name="spks.npy", mmap_mode="r", transpose=True) if channel_name == "chan1" else None
         )
 
-        self.iscell = self._load_npy("iscell.npy", mmap_mode="r")
+        # rois segmented from the iamging acquired with second channel (red/anatomical) that match the first channel segmentation
+        redcell = self._load_npy(file_name="redcell.npy", mmap_mode="r")
+        if channel_name == "chan2" and redcell is not None:
+            self.iscell = redcell
+        else:
+            self.iscell = self._load_npy("iscell.npy", mmap_mode="r")
 
         # The name of the OpticalChannel object is "OpticalChannel" if there is only one channel, otherwise it is
         # "Chan1" or "Chan2".