Aditya Pratapa adyprat
adyprat
/ labeledtif2geojson.py
Last active
May 19, 2023 20:30
convert labeled tiff to Qupath geojson v0.3.2
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| from geojson import Point, Feature, FeatureCollection, Polygon | |
| import geojson | |
| import numpy as np | |
| import tifffile | |
| import sys | |
| import pandas as pd | |
| from tqdm import tqdm | |
| import cv2 | |
| from skimage.morphology import binary_dilation |
adyprat
/ setClassFromMeasurements.groovy
Created
February 24, 2023 17:14
Set class from existing measurements in QuPath
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| import qupath.lib.scripting.QP | |
| import qupath.lib.objects.classes.PathClass | |
| def pathClasses = getQuPath().getAvailablePathClasses() | |
| print(pathClasses) | |
| for (def detection : QP.getDetectionObjects()) { | |
| def measurementList = detection.getMeasurementList() | |
| // if cluster ID is 1, the name will appear as c1 | |
| // Change prefix variable to set a diff prefix | |
| def preFix = 'c' |
adyprat
/ exportROI_QPv032.groovy
Created
March 6, 2023 15:04
QuPath export Annotation ROI script for 0.3.2
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| import qupath.lib.gui.images.servers.RenderedImageServer | |
| import qupath.lib.gui.viewer.overlays.HierarchyOverlay | |
| import qupath.lib.gui.viewer.Scalebar | |
| import qupath.lib.gui.QuPathGUI | |
| import qupath.lib.gui.viewer.OverlayOptions | |
| import qupath.lib.regions.* | |
| import ij.* | |
| import java.awt.Color | |
| import java.awt.image.BufferedImage | |
| import qupath.lib.roi.RectangleROI |
adyprat
/ exportROI_QPv042.groovy
Created
March 6, 2023 15:06
QuPath export annotation ROI for version 0.4.0 and 0.4.2
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| import qupath.lib.gui.images.servers.RenderedImageServer | |
| import qupath.lib.gui.viewer.overlays.HierarchyOverlay | |
| import qupath.lib.gui.viewer.Scalebar | |
| import qupath.lib.gui.QuPathGUI | |
| import qupath.lib.gui.viewer.OverlayOptions | |
| import qupath.lib.regions.* | |
| import ij.* | |
| import java.awt.Color | |
| import java.awt.image.BufferedImage | |
| import qupath.lib.roi.RectangleROI |
adyprat
/ labeledmat2qpjson.py
Created
March 31, 2023 18:59
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| from geojson import Point, Feature, FeatureCollection, Polygon | |
| import geojson | |
| import numpy as np | |
| import sys | |
| import pandas as pd | |
| from tqdm import tqdm | |
| import cv2 | |
| from skimage.morphology import binary_dilation | |
| from skimage import io |
adyprat
/ exportAnnotationsAsTIF.groovy
Last active
August 11, 2023 16:04
ExportQuPath Annotations As TIF
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| import qupath.lib.regions.* | |
| import ij.* | |
| import java.awt.* | |
| import java.awt.image.BufferedImage | |
| import javax.imageio.ImageIO | |
| import java.awt.Color | |
| // Set downsampling factor for saving image. Leave it at 1 for default resoluiton. | |
| // downsample of n reduces image size by 1/n. |
adyprat
/ importClassfromCsv.groovy
Created
September 5, 2023 14:27
Import the 'Class' column from a csv file using the 'Object ID' map. Expects the 'Object ID's in csv match with the ones from the QuPath image.
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| import qupath.lib.scripting.QP | |
| import qupath.lib.objects.classes.PathClass | |
| import java.io.BufferedReader | |
| import java.io.FileReader | |
| import qupath.lib.io.* | |
| def csvFilePath = Dialogs.promptForFile(null) | |
adyprat
/ exportROIv4_noLabel.groovy
Created
October 17, 2023 17:52
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| import qupath.lib.gui.images.servers.RenderedImageServer | |
| import qupath.lib.gui.viewer.overlays.HierarchyOverlay | |
| import qupath.lib.gui.viewer.Scalebar | |
| import qupath.lib.gui.QuPathGUI | |
| import qupath.lib.gui.viewer.OverlayOptions | |
| import qupath.lib.regions.* | |
| import ij.* | |
| import java.awt.Color | |
| import java.awt.image.BufferedImage | |
| import qupath.lib.roi.RectangleROI |
adyprat
/ exportROIv04.groovy
Created
October 17, 2023 17:52
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| import qupath.lib.gui.images.servers.RenderedImageServer | |
| import qupath.lib.gui.viewer.overlays.HierarchyOverlay | |
| import qupath.lib.gui.viewer.Scalebar | |
| import qupath.lib.gui.QuPathGUI | |
| import qupath.lib.gui.viewer.OverlayOptions | |
| import qupath.lib.regions.* | |
| import ij.* | |
| import java.awt.Color | |
| import java.awt.image.BufferedImage | |
| import qupath.lib.roi.RectangleROI |
adyprat
/ exportROIv05.groovy
Last active
January 3, 2024 14:48
Export annotation rendered ROI script with channel names and scale bar for QuPath v0.5.0
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| import qupath.lib.gui.images.servers.RenderedImageServer | |
| import qupath.lib.gui.viewer.overlays.HierarchyOverlay | |
| import qupath.lib.gui.viewer.Scalebar | |
| import qupath.lib.gui.QuPathGUI | |
| import qupath.lib.gui.viewer.OverlayOptions | |
| import qupath.lib.regions.* | |
| import ij.* | |
| import java.awt.Color | |
| import java.awt.image.BufferedImage | |
| import qupath.lib.roi.RectangleROI |
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