diff --git a/modules/nf-core/spotiflow/environment.yml b/modules/nf-core/spotiflow/environment.yml
deleted file mode 100644
index 8c2637dd36e..00000000000
--- a/modules/nf-core/spotiflow/environment.yml
+++ /dev/null
@@ -1,13 +0,0 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-channels:
-  - pytorch
-  - conda-forge
-  # NOTE https://github.com/nf-core/modules/issues/5813
-dependencies:
-  - cpuonly
-  - python=3.9
-  - pytorch
-  - torchvision
-  - pip:
-      - spotiflow
diff --git a/modules/nf-core/spotiflow/main.nf b/modules/nf-core/spotiflow/main.nf
index b53d60e2a47..1bf229ff0ab 100644
--- a/modules/nf-core/spotiflow/main.nf
+++ b/modules/nf-core/spotiflow/main.nf
@@ -17,9 +17,6 @@ process SPOTIFLOW {
 
     script:
     def args    = task.ext.args   ?: ''
-    def prefix  = task.ext.prefix ?: "${meta.id}"
-    def VERSION = "0.0.3"
-
     """
     spotiflow-predict \\
         ${image_2d} \\
@@ -28,20 +25,18 @@ process SPOTIFLOW {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        spotiflow: $VERSION
+        spotiflow: \$( python -m pip show --version spotiflow | grep "Version" | sed -e "s/Version: //g" )
     END_VERSIONS
     """
 
     stub:
-    def args    = task.ext.args   ?: ''
     def prefix  = task.ext.prefix ?: "${meta.id}"
-    def VERSION = "0.0.3"
     """
     touch ${prefix}.csv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        spotiflow: $VERSION
+        spotiflow: \$( python -m pip show --version spotiflow | grep "Version" | sed -e "s/Version: //g" )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/spotiflow/meta.yml b/modules/nf-core/spotiflow/meta.yml
index 96d3d001614..26fad455b6b 100644
--- a/modules/nf-core/spotiflow/meta.yml
+++ b/modules/nf-core/spotiflow/meta.yml
@@ -3,6 +3,9 @@ name: "spotiflow"
 description: Spotiflow, accurate and efficient spot detection with stereographic flow.
 keywords:
   - imaging
+  - image
+  - microscopy
+  - transcriptomics
   - spatial
   - spot
   - detection
diff --git a/modules/nf-core/spotiflow/tests/main.nf.test.snap b/modules/nf-core/spotiflow/tests/main.nf.test.snap
index 9659b9b3d37..0b52663dafd 100644
--- a/modules/nf-core/spotiflow/tests/main.nf.test.snap
+++ b/modules/nf-core/spotiflow/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e922585dfa248b3ff381e8e86674ba8c"
+                    "versions.yml:md5,699bdeeab6065da7ac70c5c7b6e4111b"
                 ],
                 "spots": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e922585dfa248b3ff381e8e86674ba8c"
+                    "versions.yml:md5,699bdeeab6065da7ac70c5c7b6e4111b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-06-12T12:06:14.300637609"
+        "timestamp": "2025-02-19T09:38:19.73403557"
     },
     "immunofluorescence - tif": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e922585dfa248b3ff381e8e86674ba8c"
+                    "versions.yml:md5,699bdeeab6065da7ac70c5c7b6e4111b"
                 ],
                 "spots": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e922585dfa248b3ff381e8e86674ba8c"
+                    "versions.yml:md5,699bdeeab6065da7ac70c5c7b6e4111b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-06-12T12:05:59.966624866"
+        "timestamp": "2025-02-19T09:38:09.947882382"
     }
 }
\ No newline at end of file