From 57b145c6ab9013213cb32a2f8b7e1992d48446a0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Thu, 3 Feb 2022 10:57:57 +0000
Subject: [PATCH] add foci_area_otsu extraction cellfun
---
extraction/core/functions/cell.py | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/extraction/core/functions/cell.py b/extraction/core/functions/cell.py
index 19f13940..5d9ca018 100644
--- a/extraction/core/functions/cell.py
+++ b/extraction/core/functions/cell.py
@@ -70,6 +70,15 @@ def max2p5pc_med(cell_mask, trap_image):
return max2p5pc / med if med else max2p5pc
+def foci_area_otsu(cell_mask, trap_image):
+ # Use otsu threshold to calculate the are of high-expression blobs inside a cell.
+ cell_pixels = trap_image[cell_mask]
+ cell_pixels = cell_pixels[~np.isnan(cell_pixels)]
+ threshold = threshold_otsu(cell_pixels)
+
+ return np.sum(cell_pixels > threshold)
+
+
def std(cell_mask, trap_image):
return np.std(trap_image[np.where(cell_mask)], dtype=float)
--
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