From aa9f80b0857ab2857a6f779d4c16bac2e560a064 Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Wed, 12 Feb 2025 13:53:41 +0100
Subject: [PATCH] Add rescaling if image is too big for Cellpose even on Naboo
---
1_identify_fibers.py | 52 ++++++++++----------------------------------
1 file changed, 11 insertions(+), 41 deletions(-)
diff --git a/1_identify_fibers.py b/1_identify_fibers.py
index ffb0f5f..cae2423 100755
--- a/1_identify_fibers.py
+++ b/1_identify_fibers.py
@@ -747,8 +747,13 @@ if __name__ == "__main__":
raw, membrane_channel, membrane_channel, 1, 1, 1, 1
)
- if not os.path.exists(str(output_dir)):
- os.makedirs(str(output_dir))
+ if (membrane.getWidth() * membrane.getHeight()) > 100000:
+ misc.timed_log("Image is too large, resizing to speed up processing")
+ membrane = membrane.resize(
+ membrane.getWidth() / 2,
+ membrane.getHeight() / 2,
+ "none",
+ )
imp_bgd_corrected = do_background_correction(membrane)
IJ.run("Conversions...", "scale")
IJ.run(imp_bgd_corrected, "16-bit", "")
@@ -764,46 +769,11 @@ if __name__ == "__main__":
perimeter_thresh=[minPer, maxPer],
)
- # update the log for the user
- misc.timed_log("Now working on " + str(raw_image_title))
- if raw_image_calibration.scaled() is False:
- IJ.log(
- "Your image is not spatially calibrated! Size measurements are only possible in [px]."
+ imp_result = imp_result.resize(
+ raw.getWidth(),
+ raw.getHeight(),
+ "none",
)
- # Only print it once since we'll use the same settings everytime
- if index == 0:
- IJ.log(" -- settings used -- ")
- IJ.log("area = " + str(minAr) + "-" + str(maxAr))
- IJ.log("perimeter = " + str(minPer) + "-" + str(maxPer))
- IJ.log("circularity = " + str(minCir) + "-" + str(maxCir))
- IJ.log("ROI expansion [microns] = " + str(enlarge_radius))
- IJ.log("Membrane channel = " + str(membrane_channel))
- IJ.log("MHC positive fiber channel = " + str(fiber_channel))
- # IJ.log("sub-tiling = " + str(tiling_factor))
- IJ.log(" -- settings used -- ")
-
- # image (pre)processing and segmentation (-> ROIs)# imp, firstC, lastC, firstZ,
- # lastZ, firstT, lastT
- membrane = Duplicator().run(raw, membrane_channel, membrane_channel, 1, 1, 1, 1)
- imp_bgd_corrected = do_background_correction(membrane)
- IJ.run("Conversions...", "scale")
- IJ.run(imp_bgd_corrected, "16-bit", "")
-
- imp_result = run_tm(
- imp_bgd_corrected,
- 1,
- cellpose_dir.getPath(),
- PretrainedModel.CYTO2,
- 30.0,
- area_thresh=[minAr, maxAr],
- circularity_thresh=[minCir, maxCir],
- perimeter_thresh=[minPer, maxPer],
- )
- IJ.saveAs(
- imp_result,
- "Tiff",
- os.path.join(output_dir, raw_image_title + "_all_fibers_binary"),
- )
IJ.saveAs(
imp_result,
--
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