From cfdf9e140e9ee554e8b558074632b893d32a0183 Mon Sep 17 00:00:00 2001 From: Yu-An Chen Date: Thu, 8 Jun 2023 07:32:02 -0700 Subject: [PATCH] Fix probability map channel reading (#22) --- large/s3seg_qc.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/large/s3seg_qc.py b/large/s3seg_qc.py index c07115e..710255b 100644 --- a/large/s3seg_qc.py +++ b/large/s3seg_qc.py @@ -61,7 +61,9 @@ def run_mcmicro( channel_names.append('Mask inner outline') if pmap_path is not None: - contour_probability_map = tifffile.imread(pmap_path, key=1) + contour_probability_map = ( + palom.reader.OmePyramidReader(pmap_path).pyramid[0][1].compute() + ) da_contour_probability_map = da.from_array( contour_probability_map, chunks=2048 )