--- a/cellpose.xml	Sat Mar 15 17:24:09 2025 +0000
+++ b/cellpose.xml	Fri Dec 12 12:36:41 2025 +0000
@@ -1,14 +1,8 @@
 <tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.02">
-    <description>with Cellpose</description>
+    <description>with Cellpose 3</description>
     <macros>
         <token name="@TOOL_VERSION@">3.1.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
-        <xml name="channel">
-            <option value="0" selected="true">grayscale/None</option>
-            <option value="1">red</option>
-            <option value="2">green</option>
-            <option value="3">blue</option>
-        </xml>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <requirements>
         <container type="docker">quay.io/biocontainers/cellpose:@TOOL_VERSION@</container>
@@ -27,7 +21,6 @@
         python '$__tool_directory__/cp_segmentation.py'
             --inputs '$inputs'
             --img_path ./image.${img_in.ext}
-            --img_format '${img_in.ext}'
             --output_dir ./segmentation
         ]]>
     </command>
@@ -35,20 +28,16 @@
         <inputs name="inputs" />
     </configfiles>
     <inputs>
-        <param name="img_in" type="data" format="ome.tiff,tiff,jpg,png" label="Choose the image file for segmention (usually after registration)"/>
+        <param name="img_in" type="data" format="ome.tiff,tiff,jpg,png" label="Choose the image file for segmentation (usually after registration)">
+            <validator type="dataset_metadata_in_range" metadata_name="channels" min="0" max="1" message="Input image is not single channel."/>
+            <validator type="dataset_metadata_in_range" metadata_name="frames" min="0" max="1" message="Input image is a multi-frame image sequence, must be a single-frame image."/>
+        </param>
         <param name="model_type" type="select" label="Choose the pre-trained model type">
             <option value="nuclei" selected="true">nuclei</option>
             <option value="cyto">cyto</option>
             <option value="cyto2">cyto2</option>
             <option value="cyto3">cyto3</option>
         </param>
-        <param argument="chan" type="select" label="Select the channel to segment" help="In this case, the default is grayscale">
-            <expand macro="channel"/>
-        </param>
-        <param argument="chan2" type="select" optional="true" label="Select the channel for nuclei segmatation" help="In this case, the default is None">
-            <expand macro="channel"/>
-        </param>
-        <param name="chan_first" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Use the reshaped data with channel as the first dimension?"/>
         <param name="show_segmentation" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Whether to show segmentation?"/>
 	    <param name="use_gpu" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to use GPU?" />
         <section name="options" title="Advanced Options" expanded="False">
@@ -72,77 +61,72 @@
     </outputs>
     <tests>
         <test expect_num_outputs="2">
-            <param name="img_in" value="img02.png"/>
+            <param name="img_in" value="img01_XY_cyto.png"/>
             <param name="model_type" value="cyto"/>
-            <param name="chan" value="2"/>
-            <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="image_diff"/>
-            <output name="cp_segm" file="img02_cp_segm_cyto.png" compare="image_diff"/>
+            <output name="cp_mask" file="img01_XY_cyto_masks.tiff" compare="image_diff"/>
+            <output name="cp_segm" file="img01_XY_cyto_segm.png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
-            <param name="img_in" value="img02.png"/>
+            <param name="img_in" value="img01_XY_cyto.png"/>
             <param name="model_type" value="cyto2"/>
-            <param name="chan" value="2"/>
-            <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_cyto2.tif" compare="image_diff"/>
-            <output name="cp_segm" file="img02_cp_segm_cyto2.png" compare="image_diff"/>
+            <output name="cp_mask" file="img01_XY_cyto2_masks.tiff" compare="image_diff"/>
+            <output name="cp_segm" file="img01_XY_cyto2_segm.png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
-            <param name="img_in" value="img02.png"/>
+            <param name="img_in" value="img01_XY_cyto.png"/>
             <param name="model_type" value="cyto3"/>
-            <param name="chan" value="2"/>
-            <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_cyto3.tif" compare="image_diff"/>
-            <output name="cp_segm" file="img02_cp_segm_cyto3.png" compare="image_diff"/>
+            <output name="cp_mask" file="img01_XY_cyto3_masks.tiff" compare="image_diff"/>
+            <output name="cp_segm" file="img01_XY_cyto3_segm.png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
-            <param name="img_in" value="img02.png"/>
+            <param name="img_in" value="img02_XY_nuclei.png"/>
             <param name="model_type" value="nuclei"/>
-            <param name="chan" value="2"/>
-            <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_nuclei.tif" compare="image_diff"/>
-            <output name="cp_segm" file="img02_cp_segm_nuclei.png" compare="image_diff"/>
+            <output name="cp_mask" file="img02_XY_nuclei_masks.tiff" compare="image_diff"/>
+            <output name="cp_segm" file="img02_XY_nuclei_segm.png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
-            <param name="img_in" value="img02.png"/>
+            <param name="img_in" value="img01_XY_cyto.png"/>
             <param name="model_type" value="cyto"/>
-            <param name="chan" value="2"/>
-            <param name="chan2" value="1"/>
-            <output name="cp_mask" file="img02_cp_masks_chan.tif" compare="image_diff"/>
-            <output name="cp_segm" file="img02_cp_segm_chan.png" compare="image_diff"/>
-        </test>
-        <test expect_num_outputs="2">
-            <param name="img_in" value="img02.png"/>
-            <param name="model_type" value="cyto"/>
-            <param name="chan" value="2"/>
-            <param name="chan2" value="3"/>
             <section name="options">
                 <param name="diameter" value="50"/>
             </section>
-            <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="image_diff"/>
-            <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="image_diff"/>
+            <output name="cp_mask" file="img01_XY_cyto_dia_masks.tiff" compare="image_diff"/>
+            <output name="cp_segm" file="img01_XY_cyto_dia_segm.png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
-            <param name="img_in" value="img02.png"/>
+            <param name="img_in" value="img01_XY_cyto.png"/>
             <param name="use_gpu" value="true"/>
             <param name="model_type" value="cyto"/>
-            <param name="chan" value="2"/>
-            <param name="chan2" value="3"/>
-            <output name="cp_mask" file="img02_cp_masks_gpu.tif" compare="image_diff"/>
-            <output name="cp_segm" file="img02_cp_segm_gpu.png" compare="image_diff"/>
+            <output name="cp_mask" file="img01_XY_cyto_gpu_masks.tiff" compare="image_diff"/>
+            <output name="cp_segm" file="img01_XY_cyto_gpu_segm.png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="img_in" value="img02.png"/>
+            <param name="img_in" value="img01_XY_cyto.png"/>
             <param name="model_type" value="cyto"/>
-            <param name="chan" value="2"/>
-            <param name="chan2" value="3"/>
             <param name="show_segmentation" value="false"/>
-            <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="image_diff"/>
+            <output name="cp_mask" file="img01_XY_cyto_masks.tiff" compare="image_diff"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="img_in" value="img03_CXY_nuclei.tiff"/>
+            <param name="model_type" value="nuclei"/>
+            <output name="cp_mask" file="img03_CXY_nuclei_masks.tiff" compare="image_diff"/>
+            <output name="cp_segm" file="img03_CXY_nuclei_segm.png" compare="image_diff"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="img_in" value="img04_XYC_nuclei.tiff"/>
+            <param name="model_type" value="nuclei"/>
+            <output name="cp_mask" file="img04_XYC_nuclei_masks.tiff" compare="image_diff"/>
+            <output name="cp_segm" file="img04_XYC_nuclei_segm.png" compare="image_diff"/>
         </test>
     </tests>
     <help>
         <![CDATA[
         Cellpose: A generalist algorithm for cell and nucleus segmentation.
+        **Important:**
+        Only singlechannel 2-D images are supported. If a channel axis is present, it must be a singleton axis (axis of length 1) and it must be either the first or the last axis within the axes layout (e.g., YX, YXC, or CYX). Other layouts are not accepted (e.g. CYXZ, XYCZ).
+        In case of multichannel images, it is necessary to priorly extract the channel for segmentation using the `Split image along axes`_ tool.
+        
+        .. _Split image along axes: ?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fimgteam%2Fsplit_image%2Fip_split_image
         ]]>
     </help>
     <citations>