Added tilesize parameter for mindagap and mindagap_duplicatefinder

CHANGELOG.md

@@ -3,6 +3,22 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.1dev - [2023.25.10]
+
+Implemented the tilesize parameter for Mindagap_mindagap and mindagap_duplicatefinder so that smaller representative images can be used as test.
+
+### `Added`
+
+- tilesize param
+- tilesize passing to mindagap and duplicatefinder in modules.config
+-
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.0.1dev - [2023.23.10]
 
 - Replace `PROJECT_SPOTS` and `MCQUANT` modules with spot2cells. This new (for now local) module reduces the RAM requirements drastically, because it doesn't create a multi-channel stack for the spots. Spots are assigned by looking up cell IDs at x,y, positions and iterating over the deduplicated spots table.

conf/modules.config

@@ -49,6 +49,18 @@ process {
         ]
     }
 
+    withName: "MINDAGAP_MINDAGAP" {
+        ext.args = [ "",
+            params.tilesize ? "-xt ${params.tilesize}" : ""
+        ].join(" ").trim()
+    }
+
+    withName: "MINDAGAP_DUPLICATEFINDER" {
+        ext.args = [ "",
+            params.tilesize ? "${params.tilesize}" : ""
+        ].join(" ").trim()
+    }
+
     withName: "CREATETRAININGTIFF" {
         publishDir = [
             path: { "${params.outdir}/training_subset/tiff" }

nextflow.config

@@ -29,6 +29,7 @@ params {
 
 
     // Preprocessing command line flags
+    tilesize                   = 2144
     skip_clahe                 = false
     clahe_cliplimit            = 0.01
     clahe_nbins                = 256

nextflow_schema.json

@@ -90,10 +90,10 @@
             "required": ["segmentation_method"],
             "fa_icon": "fas fa-border-all"
         },
-        "contrast_adjustment": {
-            "title": "Contrast adjustment",
+        "image_preprocessing": {
+            "title": "Image preprocessing",
             "type": "object",
-            "description": "Define should contrast adjustment be applied and how.",
+            "description": "Defines gridsize for Mindagap and should contrast adjustment be applied and how.",
             "default": "",
             "fa_icon": "fas fa-adjust",
             "properties": {
@@ -125,6 +125,12 @@
                     "type": "boolean",
                     "description": "Specifies whether contrast-limited adaptive histogram equalization should be skipped.",
                     "fa_icon": "fab fa-buromobelexperte"
+                },
+                "tilesize": {
+                    "type": "integer",
+                    "default": 2144,
+                    "description": "Tile size (distance between gridlines)",
+                    "fa_icon": "fas fa-th"
                 }
             }
         },
@@ -405,7 +411,7 @@
             "$ref": "#/definitions/segmentation_methods_and_options"
         },
         {
-            "$ref": "#/definitions/contrast_adjustment"
+            "$ref": "#/definitions/image_preprocessing"
         },
         {
             "$ref": "#/definitions/training_subset_options"