From bd18e5b768686f3d6dbd57d4c37b8e6d4ecf64a9 Mon Sep 17 00:00:00 2001
From: Alessandra Trapani <55453048+alessandratrapani@users.noreply.github.com>
Date: Fri, 5 Jan 2024 16:40:32 +0100
Subject: [PATCH] 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 <51133164+CodyCBakerPhD@users.noreply.github.com>
---
 .../extractors/suite2p/suite2psegmentationextractor.py     | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py b/src/roiextractors/extractors/suite2p/suite2psegmentationextractor.py
index 5756a32f..070d132c 100644
--- 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".