Migration04 rg

Analyze/Spatial Analysis/Compute_detection_distance_to_annotation_border.groovy

@@ -2,8 +2,11 @@
  * Get the distance of each detection to its parent's edge
  * 
  * @author Olivier Burri
- * @date 202211009
- * Last tested on QuPath-0.3.2
+ * @date 20221207
+ * Last tested on QuPath-0.4 (RG 20221207)
+ * 
+ * Requires at least 1 annotation and cells in it 
+ * 
  */
 
 def annotations = getAnnotationObjects()

Analyze/StarDist/Create_training_rectangle.groovy

@@ -4,10 +4,12 @@
  * SHIFT + D to create more and move them across the image.
  * @author Olivier Burri
  * Date: 2020.09.15
+ * 
+ * Last tested on QuPath-0.4 (RG 20221207)
  */
 
 // PARAMETERS
-def size = 256 // in pixels: the size of the rectangle (width and height) to create.
+def size = 1024 // in pixels: the size of the rectangle (width and height) to create.
 
 
 // Script start

Analyze/StarDist/Export_annotations_for_StarDist_training.groovy

@@ -28,13 +28,13 @@ respectively. The naming convention was chosen to match the one used for the Sta
 
 Authors: Olivier Burri, Romain Guiet BioImaging and Optics Platform (EPFL BIOP)
 
-Tested on QuPath 0.3.2, 2022.04.13
+Tested on QuPath 0.4.0, 2022.12.08 (RG)
 
 Due to the simple nature of this code, no copyright is applicable
 */
 
 // USER SETTINGS
-def channel_of_interest = 2 // null to export all the channels 
+def channel_of_interest = 1 // null to export all the channels 
 def downsample = 1
 
 

Analyze/StarDist/Run_brightfield_StarDist_detection_using_HE_model.groovy

@@ -1,9 +1,14 @@
-import qupath.ext.stardist.StarDist2D
+/*
+ * Tested on QuPath 0.4.0, 2022.12.08 (RG)
+/*
+ * Tested on QuPath 0.4.0, 2022.12.08 (RG)
+ */
+ import qupath.ext.stardist.StarDist2D
 clearDetections()
 
 // Specify the model file (you will need to change this!)
-var pathModel = 'C:/QuPath_Common_Data_0.3/models/he_heavy_augment.pb'
-//var pathModel = 'C:/QuPath_Common_Data_0.3/models/dsb2018_heavy_augment.pb'
+var pathModel = 'C:/QuPath_Common_Data_0.4/models/he_heavy_augment.pb'
+//var pathModel = 'C:/QuPath_Common_Data_0.4/models/dsb2018_heavy_augment.pb'
 
 // Get current image - assumed to have color deconvolution stains set
 var imageData = getCurrentImageData()

Analyze/StarDist/Run_brightfield_StarDist_detection_using_dsb2018_model.groovy

@@ -1,8 +1,13 @@
+
+/*
+ * Tested on QuPath 0.4.0, 2022.12.08 (RG)
+ */
+
 import qupath.ext.stardist.StarDist2D
 
 // Specify the model file (you will need to change this!)
-//var pathModel = 'C:/QuPath_Common_Data_0.3/models/he_heavy_augment.pb'
-var pathModel = 'C:/QuPath_Common_Data_0.3/models/dsb2018_heavy_augment.pb'
+//var pathModel = 'C:/QuPath_Common_Data_0.4/models/he_heavy_augment.pb'
+var pathModel = 'C:/QuPath_Common_Data_0.4/models/dsb2018_heavy_augment.pb'
 
 // Get current image - assumed to have color deconvolution stains set
 var imageData = getCurrentImageData()

Analyze/StarDist/Run_default_StarDist_detection.groovy

@@ -1,15 +1,17 @@
+/*
+ * Tested on QuPath 0.4.0, 2022.12.08 (RG)
+ */
 
-
-import qupath.tensorflow.stardist.StarDist2D
+//import qupath.tensorflow.stardist.StarDist2D
+import qupath.ext.stardist.StarDist2D
 
 // Specify the model directory (you will need to change this!)
-//def pathModel = 'Z:\\public\\0 - BIOP Data\\StarDist Models\\silvia_rat_brain_deconvolved_usr_augment_r32_p256_g2_e400_se100_b8_aug_challenge'
-def pathModel = 'C:\\Users\\oburri\\Desktop\\he_heavy_augment.pb'
+def pathModel = 'C:/QuPath_Common_Data_0.4/models/dsb2018_heavy_augment.pb'
 
 
 def stardist = StarDist2D.builder(pathModel)
         .threshold(0.4)              // Probability (detection) threshold
-        .channels('Original')            // Select detection channel
+        .channels('DAPI')            // Select detection channel
         .normalizePercentiles(1, 99.8) // Percentile normalization
         .pixelSize(0.5)              // Resolution for detection
 //        .tileSize(2048)              // Specify width & height of the tile used for prediction

Analyze/StarDist/Run_fluorescent_StarDist_detection_using_dsb2018_model.groovy

@@ -1,8 +1,11 @@
-import qupath.ext.stardist.StarDist2D
+/*
+ * Tested on QuPath 0.4.0, 2022.12.08 (RG)
+ */
+ import qupath.ext.stardist.StarDist2D
 
 // Specify the model file (you will need to change this!)
-//var pathModel = 'C:/QuPath_Common_Data_0.3/models/he_heavy_augment.pb'
-var pathModel = 'C:/QuPath_Common_Data_0.3/models/dsb2018_heavy_augment.pb'
+//var pathModel = 'C:/QuPath_Common_Data_0.4/models/he_heavy_augment.pb'
+var pathModel = 'C:/QuPath_Common_Data_0.4/models/dsb2018_heavy_augment.pb'
 
 // Get current image - assumed to have color deconvolution stains set
 var imageData = getCurrentImageData()

Analyze/StarDist/Run_qupath_cell_detection_and_convert_to_annotations.groovy

@@ -7,6 +7,11 @@
  *
  * @author Olivier Burri
  * Date: 2020.09.15
+ * 
+ * 
+ * Tested on QuPath 0.4.0, 2022.12.08 (RG)
+ *
+ * 
  */
 
 clearDetections()
@@ -16,8 +21,7 @@ def toDelete = getAllObjects().findAll{ !(it.getROI() instanceof RectangleROI )
 removeObjects( toDelete, false )
 
 // Put the cell detection script between the accolades {}
-cellDetection = { runPlugin('qupath.imagej.detect.cells.WatershedCellDetection', '{"detectionImage": "DAPI",  "requestedPixelSizeMicrons": 0.1302,  "backgroundRadiusMicrons": 5.0,  "medianRadiusMicrons": 0.0,  "sigmaMicrons": 2.4,  "minAreaMicrons": 40.0,  "maxAreaMicrons": 1000.0,  "threshold": 1600.0,  "watershedPostProcess": true,  "cellExpansionMicrons": 1.1,  "includeNuclei": true,  "smoothBoundaries": true,  "makeMeasurements": true}'); }
-
+cellDetection = { runPlugin('qupath.imagej.detect.cells.WatershedCellDetection', '{"detectionImage":"DAPI","requestedPixelSizeMicrons":0.5,"backgroundRadiusMicrons":8.0,"backgroundByReconstruction":true,"medianRadiusMicrons":0.0,"sigmaMicrons":1.5,"minAreaMicrons":10.0,"maxAreaMicrons":400.0,"threshold":25.0,"watershedPostProcess":true,"cellExpansionMicrons":1.0,"includeNuclei":true,"smoothBoundaries":true,"makeMeasurements":true}') }
 // Script starts below
 
 // Select all annotations, ideally 

View/Set_fluorescent_channel_names_ranges_and_colors.groovy

@@ -5,28 +5,31 @@
  *
  * @author Olivier Burri
  * @date 20221103
- * Last tested on QuPath-0.3.2
+ * 
+ * Tested on QuPath 0.4.0, 2022.12.08 (RG)
+ * 
  */
 
 setImageType('FLUORESCENCE')
 
 // You can replace the names with your stainings if you want
 
 // Channel names in order
-def names = ['DAPI', 'FITC', 'CY3', 'CY5']
+def names = ['DAPI', 'FITC', 'CY3', 'CY5',"CY7"]
 
 // Channel minimum display values, in order
-def mins = [ 0, 0, 0, 0 ]
+def mins = [ 0, 0, 0, 0 , 0]
 
 // Channel maximum display values, in order
-def maxs = [ 8000, 7500, 6000, 820 ]
+def maxs = [ 255, 255, 255, 255,255 ]
 
 // Channel colors: Make sure that the number of colors in this list
 // matches the number of channels
 def colors = [ getColorRGB( 0, 128, 255 ),
                getColorRGB( 0, 255, 128 ),
-               getColorRGB( 128, 255, 0 ),
-               getColorRGB( 255, 0, 128 )
+               getColorRGB( 255, 128, 0 ),
+               getColorRGB( 255, 0, 128 ),
+               getColorRGB( 128, 0, 255 )
              ]