romainGuiet
/ WSI_GuidedTour_Display.groovy
Created
March 12, 2026 07:44
Allow to display a Guided Tour of a WSI set using tjhe script WSI_GuidedTour_Store.groovy
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| // === UI Components === | |
| TextArea textDisplay = new TextArea() | |
| textDisplay.setEditable(false) | |
| textDisplay.setWrapText(true) | |
| textDisplay.setPrefRowCount(5) | |
| VBox channelInfoBox = new VBox(5) | |
| channelInfoBox.setStyle("-fx-padding: 5; -fx-border-color: lightgray; -fx-border-width: 1;") | |
| Label channelInfoLabel = new Label("Displayed Channels") | |
| channelInfoLabel.setStyle("-fx-font-weight: bold;") |
romainGuiet
/ WSI_GuidedTour_Store.groovy
Created
March 12, 2026 07:42
Allow storing description and display settings in the description field of a annotation. Use the script WSI_GuidedTour_Display.groovy to play them
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| // === UI Components === | |
| // LEFT SIDE | |
| Label annotationLabel = new Label("Name") | |
| TextField annotationNameField = new TextField() | |
| Label descriptionLabel = new Label("Description") | |
| TextArea descriptionField = new TextArea() | |
| descriptionField.setPrefRowCount(10) | |
| descriptionField.setWrapText(true) | |
| descriptionField.setPrefColumnCount(20) |
romainGuiet
/ COMET_QC_Graph.groovy
Last active
March 12, 2026 07:40
A groovy script for QuPath to quickly create a graph with channels of interest, to visualize pixel intensities in defined annotations.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import javafx.application.Application | |
| import javafx.scene.Scene | |
| import javafx.scene.control.* | |
| import javafx.scene.layout.GridPane | |
| import javafx.stage.Stage | |
| import javafx.scene.chart.NumberAxis | |
| import javafx.scene.chart.ScatterChart | |
| import javafx.scene.chart.XYChart | |
| import javafx.scene.paint.Color | |
| import javafx.scene.shape.Circle |
romainGuiet
/ 2tabs_1LoadCSV_2LoadPoints_v0.groovy
Last active
February 5, 2026 09:02
a QuPath GUI to load points from csv file
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import javafx.application.Platform | |
| import javafx.scene.Scene | |
| import javafx.scene.control.* | |
| import javafx.scene.layout.* | |
| import javafx.stage.Stage | |
| import javafx.stage.DirectoryChooser | |
| import javafx.geometry.Insets | |
| import javafx.geometry.Pos | |
| import javafx.collections.FXCollections | |
| import javafx.collections.ObservableList |
romainGuiet
/ minimal_cellpose_analysis.ijm
Created
October 21, 2025 07:24
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| //PARAMETERS | |
| nuclei_ch = 3 | |
| measure_ch = 1 | |
| conda_env_path = "D:/conda/conda-envs/cellpose-3111" // replace with the path to your cellpose environment | |
| image_title = getTitle(); | |
| // do some cleaning | |
| roiManager("reset"); | |
| run("Clear Results"); |
romainGuiet
/ make_movie.groovy
Created
August 21, 2025 13:25
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #@ File(style="directory") dir | |
| frames = 3 | |
| IJ.run("Close All", ""); | |
| ArrayList<ImagePlus> imps = new ArrayList<>(frames); | |
| dir.eachFile { | |
| //println(it) |
romainGuiet
/ random_boxes_in_annotation.groovy
Last active
August 21, 2025 08:54
The script expects to find a "Tissue" annotation (optionally this annotation can be generated it via a PixelClassifier, line 40 ) , and then creates defined nbr of boxes in the annotation. #biop #qupath
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| // Change the name of the tissue classifier here if needed | |
| def tissueFinder = "Tissue" | |
| // Which Name should they have ? | |
| // if annotation with the same name exist they will be deleted | |
| def annotation_name = "Analysis" | |
romainGuiet
/ thresholds_familiy.ijm
Created
June 17, 2025 11:18
show that different thresholds can output similar results
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| // clear the environment | |
| run("Close All"); | |
| roiManager("Reset"); | |
| //open an image | |
| run("Fly Brain (1MB)"); | |
| // make it composite, duplicate one slice and get information | |
| run("Make Composite"); | |
| run("Duplicate...", "duplicate channels=1 slices=27"); | |
| getDimensions(width, height, channels, slices, frames); |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| // clear the environment | |
| run("Close All"); | |
| run("Clear Results") | |
| roiManager("Reset"); | |
| // Set the measurements of intererest | |
| run("Set Measurements...", "area mean standard min limit display redirect=None decimal=3"); | |
| run("Gel (105K)"); | |
| rename("Original"); |
romainGuiet
/ BIOP_Flatfield_And_Stitch.groovy
Created
June 16, 2025 14:56
It is often the case that tiled microscopy images contain artifacts due to uneven illumination. This is due to the shape of the illumination, the quality of the optics and the size of the field of view
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #@File(label="Multiposition Files Directory",style="directory") image_directory | |
| #@String(value="Select a file for flat field correction or write none", visibility="MESSAGE") textFF | |
| #@File(label="Flatfield Stack File") ff_file | |
| #@int(label="Downsample Factor", style = "slider", min = 1, max = 16, stepSize = 1) downsample | |
| #@Boolean(label="Perform Stitching") is_do_stitch | |
| #@Boolean(label="Compute Overlap") is_compute | |
| #@Boolean(label="Keep Original Bit Depth") is_keep_bit_depth | |
| #@String(label="Macro Mode",choices={"Fuse and display","Write to disk"}) output_type | |
| #@Boolean(label="Save final stitched as *.ids (if write to disk)") save_Stiched_asIDS | |
| #@Boolean(label="Delete temporary files (if write to disk)") delete_temp_files |
NewerOlder