Caner Ercan caner-ercan
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| /* | |
| Purpose: | |
| This QuPath script exports annotations to a CSV file in a format compatible with Polyscope. | |
| The output file must be copied into the following directory in Polyscope: | |
| `..//polyscope/polyzoomer/PathXXXX_XXX/page/imagename/_imagename/annotations.txt` | |
| Works with any version of QuPath—until further notice (or disaster). | |
| Author: Caner Ercan | |
| Date: 28.02.2025 |
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| base_path = "B:/data/BE/cell_detect/acformer/" | |
| collected_data = NULL | |
| for (dataset in c("NU_dataset_rois","MDA1_dataset_rois","MDA2_dataset_rois")){ | |
| txt_path = paste(base_path,dataset ,"img_list.txt",sep="/") | |
| print(txt_path) | |
| txt_table = read.table(txt_path) |
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| def classes2delete = ["tissue_box", "tissue"] | |
| classes2delete.each { delclass -> | |
| print delclass | |
| toRemove = getAnnotationObjects().findAll { | |
| it.getPathClass()==getPathClass(delclass) | |
| removeObject(it, true) | |
| } | |
caner-ercan
/ export_roi_point2csv_relative2roi.groovy
Created
September 4, 2024 01:12
export points
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| resolveHierarchy() | |
| def server = getCurrentServer() | |
| tsv_folder = buildFilePath(PROJECT_BASE_DIR, "tsv") | |
| def checkDir = new File(tsv_folder) | |
| if(!checkDir.exists()) { | |
| checkDir.mkdir() | |
| } | |
| csv_folder = buildFilePath(PROJECT_BASE_DIR, "corrected_point") | |
| checkDir = new File(csv_folder) |
caner-ercan
/ featch_annotation_info.sh
Last active
January 5, 2025 23:16
QuPath data access via json
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| #!/bin/bash | |
| # Define the base directory | |
| BASE_DIR="/Users/cercan/Desktop/BE/NU_wholeDataset_qupath/data" # Change this to your target directory | |
| OUTPUT_CSV="/Users/cercan/Desktop/BE/NU_wholeDataset_qupath/annotationData.csv" | |
| # Write the header to the CSV file | |
| echo "Name,Unclassified,Biopsy,Flow" > "$OUTPUT_CSV" | |
| # Find all subdirectories and process the JSON files |
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| import org.apache.commons.io.FilenameUtils | |
| def name = FilenameUtils.getBaseName(getProjectEntry().getImageName()) | |
| def server = getCurrentServer() | |
| selectObjectsByClassification("flow") | |
| anns =[] | |
| def anns = getSelectedObjects() | |
| i=0 | |
| for (ann in anns) { | |
| def roi = ann.getROI() |
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| //0.2.0 version of https://forum.image.sc/t/assign-point-objects-to-different-rois-by-overlap/26905/2?u=research_associate | |
| // Convert points into detections, resolve the heirarchy so they are now child objects of any annotations. | |
| import qupath.lib.roi.EllipseROI; | |
| import qupath.lib.objects.PathDetectionObject | |
| points = getAnnotationObjects().findAll{it.getROI().isPoint() } | |
| print points[0].getROI() | |
| describe(points[0].getROI()) |
caner-ercan
/ StarDistDetection_calculation.groovy
Last active
February 16, 2024 16:53
#StarDist Cell Detection #QuPath
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| //don't forget to change the stardist model location | |
| // this script will detect the cells and calculate shape, intensity features | |
| // iff you have a cell classifier model you can add it too at line 53 | |
| // the output measurements will be in a folder named 'cellMeasurements' in the project directory | |
| //caner 15.02.23 | |
| import qupath.ext.stardist.StarDist2D | |
| import qupath.lib.images.servers.* | |
| // Specify the model directory (you will need to change this!) |
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| //* | |
| //Caner Ercan | |
| //[email protected] | |
| //First Dialog Asks for the folder which contains all the images | |
| //Second dialog asks for time zero image | |
| //It generates a file in the same folder named as Results.csv | |
| *// | |
| setBatchMode(true); | |
| input = getDirectory("Choose Image Directory"); |
caner-ercan
/ Alignment - MultiFile Distribute to all other images.groovy
Last active
February 16, 2024 17:04
— forked from Svidro/!Manipulating objects in QuPath
Manipulating objects in #QuPath
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| /** | |
| From https://forum.image.sc/t/qupath-multiple-image-alignment-and-object-transfer/35521/2 | |
| 0.2.0m9 | |
| If you have annotations within annotations, you may get duplicates. Ask on the forum or change the def pathObjects line. | |
| To use, have all objects desired in one image, and alignment files in the Affine folder within your project folder. | |
| If you have not saved those, this script will not work. | |
| It will use ALL of the affine transforms in that folder to transform the objects in the current image to the destination images | |
| that are named after the affine files. |
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