From 86c76c924d0c4592da92371002c5bd5fd2f19b19 Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Mon, 15 Jun 2026 15:01:29 +0200
Subject: [PATCH] =?UTF-8?q?fix(trackmate):=20=F0=9F=90=9B=20fix=20TrackMat?=
 =?UTF-8?q?e=20settings=20and=20label=20image=20output?=
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---
 .gitignore                       |  1 +
 src/imcflibs/imagej/trackmate.py | 11 ++++++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 7125412e..6e22d86a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -118,3 +118,4 @@ docs/api/*
 docs/_build/*
 cover/*
 MANIFEST
+AGENTS.md
\ No newline at end of file
diff --git a/src/imcflibs/imagej/trackmate.py b/src/imcflibs/imagej/trackmate.py
index 7f16b325..1148ef14 100644
--- a/src/imcflibs/imagej/trackmate.py
+++ b/src/imcflibs/imagej/trackmate.py
@@ -69,6 +69,13 @@ def cellpose_detector(
     ...    optional_channel=0
     ... )
     """
+
+    dims = imageplus.getDimensions()
+    cal = imageplus.getCalibration()
+
+    if imageplus.getNSlices() > 1:
+        imageplus.setDimensions(dims[2], dims[4], dims[3])
+
     settings = Settings(imageplus)
 
     settings.detectorFactory = CellposeDetectorFactory()
@@ -94,10 +101,12 @@ def cellpose_detector(
         return
 
     settings.detectorSettings["CELLPOSE_MODEL"] = selected_model
-    settings.detectorSettings["CELL_DIAMETER"] = obj_diameter
+    settings.detectorSettings["CELL_DIAMETER"] = Double(obj_diameter)
     settings.detectorSettings["USE_GPU"] = use_gpu
     settings.detectorSettings["SIMPLIFY_CONTOURS"] = simplify_contours
 
+    imageplus.setDimensions(dims[2], dims[3], dims[4])
+
     return settings