update example scripts

BIOP · Dec 9, 2024 · 361870a · 361870a
1 parent 9604bce
commit 361870a
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/resources/scripts/cellpose_macro.ijm b/resources/scripts/cellpose_macro.ijm
@@ -1,5 +1,5 @@
-conda_env_path = "D:/conda/conda-envs/cellpose-307-gpu"
+#@File(style="directory" , label="Select conda environment") conda_env_path
 //run("Blobs (25K)"); // uncomment to test
 image_title = getTitle();
 
-run("Cellpose ..." ,"imp="+image_title+" conda_env_path="+conda_env_path+" diameter=30 model=cyto3 model_path= ch1=1 ch2=1 additional_flags=--use_gpu" );
+run("Cellpose ..." ,"imp="+image_title+" conda_env_path="+conda_env_path+" env_type=conda diameter=30 model=cyto3 model_path= ch1=1 ch2=1 additional_flags=--use_gpu" );
diff --git a/resources/scripts/cellpose_script.groovy b/resources/scripts/cellpose_script.groovy
@@ -11,7 +11,7 @@ IJ.runMacro("close('\\\\Others');")
 
 // cellpose parameters
 def cp = new Cellpose();
-cp.conda_env_path = conda_env_path
+cp.env_path = conda_env_path
 // Or comment the line avove and set the path manually
 // to locate your conda env from a terminal type "conda env list", it will return the path you can paste below
 //cp.conda_env_path = new File ( "D:/conda/conda_envs/cellpose/" ) ;
@@ -20,7 +20,8 @@ cp.diameter = 50;
 cp.model = "cyto3";
 cp.ch1 = 1 ;
 cp.ch2 = 2 ;
-cp.additional_flags= "--use_gpu, --do_3D, --anisotropy, 4 , --restore_type , denoise_cyto3";
+//cp.additional_flags= "--use_gpu, --do_3D, --anisotropy, 4 , --restore_type , denoise_cyto3";
+cp.additional_flags= "--use_gpu,  --restore_type , denoise_cyto3";
 // cellpose run
 cp.run();
 // get the output labels image
@@ -35,4 +36,4 @@ cp_imp.setDisplayRange(0, 12);
 return
 
 import ch.epfl.biop.wrappers.cellpose.ij2commands.Cellpose
-import ij.IJ;
+import ij.IJ;