diff --git a/src/main/java/fiji/plugin/trackmate/cellpose/AbstractCellposeSettings.java b/src/main/java/fiji/plugin/trackmate/cellpose/AbstractCellposeSettings.java
index a17885bf..4eb60be5 100644
--- a/src/main/java/fiji/plugin/trackmate/cellpose/AbstractCellposeSettings.java
+++ b/src/main/java/fiji/plugin/trackmate/cellpose/AbstractCellposeSettings.java
@@ -1,9 +1,12 @@
 package fiji.plugin.trackmate.cellpose;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
+import ij.IJ;
+
 public abstract class AbstractCellposeSettings
 {
 
@@ -88,6 +91,14 @@ public List< String > toCmdLine( final String imagesDir )
 		final String lastItem = split[ split.length - 1 ];
 		if ( lastItem.toLowerCase().startsWith( "python" ) )
 		{
+			// Activate conda env if it runs in Windows.
+			if ( IJ.isWindows() )
+			{
+				final String envname = split[ split.length - 2 ];
+				cmd.addAll( Arrays.asList( "cmd.exe", "/c", "conda", "activate", envname ) );
+				cmd.add( "&" );
+			}
+
 			// Calling Cellpose from python.
 			cmd.add( executablePath );
 			cmd.add( "-m" );