A B C G H I L M N O P R S U W
All Classes All Packages

A

acronym - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

actionABBA - Variable in class ch.epfl.biop.qupath.extension.BIOPExtension.ABBACommands

actionApplyDisplay - Variable in class ch.epfl.biop.qupath.extension.BIOPExtension.DisplayCommands

actionRNAScope - Variable in class ch.epfl.biop.qupath.extension.BIOPExtension.RNAScopeCommands

addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class ch.epfl.biop.qupath.analysis.RNAScopeCounts2

addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

addShapeStatistics(MeasurementList, Roi, ImageProcessor, Calibration, String) - Static method in class ch.epfl.biop.qupath.utils.internal.ObjectMeasurements

addShapeStatistics(MeasurementList, PolygonROI, double, double, String) - Static method in class ch.epfl.biop.qupath.utils.internal.ObjectMeasurements

Add basic shape measurements to a MeasurementList.

AllenBrainRegion() - Constructor for class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

AllenOntologyJson - Class in ch.epfl.biop.atlas.allen

AllenOntologyJson() - Constructor for class ch.epfl.biop.atlas.allen.AllenOntologyJson

AllenOntologyJson.AllenBrainRegion - Class in ch.epfl.biop.atlas.allen

ApplyDisplaySettingsCommand - Class in ch.epfl.biop.qupath.commands

ApplyDisplaySettingsCommand(QuPathGUI) - Constructor for class ch.epfl.biop.qupath.commands.ApplyDisplaySettingsCommand

atlas_id - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

AtlasTools - Class in ch.epfl.biop.qupath.atlas.allen.api

AtlasTools() - Constructor for class ch.epfl.biop.qupath.atlas.allen.api.AtlasTools

B

BIOPExtension - Class in ch.epfl.biop.qupath.extension

BIOPExtension - Class in ch.epfl.biop.qupath.utils.internal

BIOPExtension() - Constructor for class ch.epfl.biop.qupath.extension.BIOPExtension

BIOPExtension() - Constructor for class ch.epfl.biop.qupath.utils.internal.BIOPExtension

BIOPExtension.ABBACommands - Class in ch.epfl.biop.qupath.extension

BIOPExtension.DisplayCommands - Class in ch.epfl.biop.qupath.extension

BIOPExtension.RNAScopeCommands - Class in ch.epfl.biop.qupath.extension

Commands based on OpenCV.

C

ch.epfl.biop.atlas.allen - package ch.epfl.biop.atlas.allen

ch.epfl.biop.qupath.analysis - package ch.epfl.biop.qupath.analysis

ch.epfl.biop.qupath.atlas.allen.api - package ch.epfl.biop.qupath.atlas.allen.api

ch.epfl.biop.qupath.atlas.allen.commands - package ch.epfl.biop.qupath.atlas.allen.commands

ch.epfl.biop.qupath.atlas.allen.utils - package ch.epfl.biop.qupath.atlas.allen.utils

ch.epfl.biop.qupath.commands - package ch.epfl.biop.qupath.commands

ch.epfl.biop.qupath.extension - package ch.epfl.biop.qupath.extension

ch.epfl.biop.qupath.utils - package ch.epfl.biop.qupath.utils

ch.epfl.biop.qupath.utils.internal - package ch.epfl.biop.qupath.utils.internal

children - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

color_hex_triplet - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

createCellObjects(PathObject, List<PathObject>, double) - Static method in class ch.epfl.biop.qupath.utils.PathUtils

G

getAllMeasurements() - Static method in class ch.epfl.biop.qupath.utils.Utils

Returns all the measurements available in QuPath for the all pathObjects Then we can use things like getStringValue() and getDoubleValue()

getAllMeasurements(List<PathObject>) - Static method in class ch.epfl.biop.qupath.utils.Utils

Creates an ObservableMeasurementTableData for the requested PathObjects

getArea(PathObject) - Static method in class ch.epfl.biop.qupath.utils.PathUtils

returns the area of the current PathObject in pixels If the area is not defined (like points) it returns 0

getAreaMicrons(PathObject) - Static method in class ch.epfl.biop.qupath.utils.PathUtils

returns the area of the current PathObject in calibrated units.

getDefaultParameterList(ImageData<BufferedImage>) - Method in class ch.epfl.biop.qupath.analysis.RNAScopeCounts2

getDescription() - Method in class ch.epfl.biop.qupath.analysis.RNAScopeCounts2

getDescription() - Method in class ch.epfl.biop.qupath.extension.BIOPExtension

getDescription() - Method in class ch.epfl.biop.qupath.utils.internal.BIOPExtension

getDescription() - Method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

getFlattenedWarpedAtlasRegions(ImageData) - Static method in class ch.epfl.biop.qupath.atlas.allen.api.AtlasTools

getFullImageAnnotation() - Static method in class ch.epfl.biop.qupath.utils.PathUtils

returns a rectangle with teh whole dataset as an annotation.

getImagePlus(PathObject, int) - Static method in class ch.epfl.biop.qupath.utils.GUIUtils

getImagePlus(PathObject, int, boolean, boolean) - Static method in class ch.epfl.biop.qupath.utils.GUIUtils

getImagePlus(PathObject, int, boolean, boolean, boolean, boolean) - Static method in class ch.epfl.biop.qupath.utils.GUIUtils

getLastResultsDescription() - Method in class ch.epfl.biop.qupath.analysis.RNAScopeCounts2

getLastResultsDescription() - Method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

getName() - Method in class ch.epfl.biop.qupath.analysis.RNAScopeCounts2

getName() - Method in class ch.epfl.biop.qupath.extension.BIOPExtension

getName() - Method in class ch.epfl.biop.qupath.utils.internal.BIOPExtension

getName() - Method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

getOntologyFromFile(File) - Static method in class ch.epfl.biop.atlas.allen.AllenOntologyJson

getParameterList(ImageData<BufferedImage>) - Method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

getParentObjects(PluginRunner<BufferedImage>) - Method in class ch.epfl.biop.qupath.analysis.RNAScopeCounts2

getParentObjects(PluginRunner<BufferedImage>) - Method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

getPixelSize() - Static method in class ch.epfl.biop.qupath.utils.Utils

Returns the current pixel size of the active image in microns

getRegionFromId(int) - Method in class ch.epfl.biop.atlas.allen.AllenOntologyJson

getSelectedChannelsServer(ImageServer, List<String>) - Static method in class ch.epfl.biop.qupath.utils.GUIUtils

getSupportedParentObjectClasses() - Method in class ch.epfl.biop.qupath.analysis.RNAScopeCounts2

getSupportedParentObjectClasses() - Method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

graph_order - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

GUIUtils - Class in ch.epfl.biop.qupath.utils

Here we store a bunch of utility functions that are relevant to QuPath's User interface Like setting colors, lookup tables and such

GUIUtils() - Constructor for class ch.epfl.biop.qupath.utils.GUIUtils

H

hemisphere_id - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

I

id - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

ImageJMacroRunner - Class in ch.epfl.biop.qupath.utils.internal

QuPath plugin for running ImageJ macros & returning detected regions.

ImageJMacroRunner(QuPathGUI) - Constructor for class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

Constructor.

ImportLegacyRelativeProject - Class in ch.epfl.biop.qupath.commands

ImportLegacyRelativeProject() - Constructor for class ch.epfl.biop.qupath.commands.ImportLegacyRelativeProject

installExtension(QuPathGUI) - Method in class ch.epfl.biop.qupath.extension.BIOPExtension

installExtension(QuPathGUI) - Method in class ch.epfl.biop.qupath.utils.internal.BIOPExtension

L

LineToArea(ROI, double) - Static method in class ch.epfl.biop.qupath.utils.PathUtils

Converts a line to a very thin 4 sided polygon, so it has an area

LoadAtlasRoisToQuPathCommand - Class in ch.epfl.biop.qupath.atlas.allen.commands

LoadAtlasRoisToQuPathCommand(QuPathGUI) - Constructor for class ch.epfl.biop.qupath.atlas.allen.commands.LoadAtlasRoisToQuPathCommand

loadWarpedAtlasAnnotations(ImageData) - Static method in class ch.epfl.biop.qupath.atlas.allen.api.AtlasTools

M

main(String...) - Static method in class ch.epfl.biop.atlas.allen.AllenOntologyJson

mergePathObjects(List<PathObject>) - Static method in class ch.epfl.biop.qupath.utils.PathUtils

mergeTouchingPathObjects(List<PathObject>) - Static method in class ch.epfl.biop.qupath.utils.PathUtils

This method tries to merge all the pathobjects that are touching, but keeping all others intact

N

name - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

O

ObjectMeasurements - Class in ch.epfl.biop.qupath.utils.internal

ObjectMeasurements() - Constructor for class ch.epfl.biop.qupath.utils.internal.ObjectMeasurements

ontology_id - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

openRoiSet(File) - Static method in class ch.epfl.biop.qupath.atlas.allen.utils.RoiSetLoader

P

parent_structure_id - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

parseArgument(ImageData<BufferedImage>, String) - Method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

PathUtils - Class in ch.epfl.biop.qupath.utils

PathUtils() - Constructor for class ch.epfl.biop.qupath.utils.PathUtils

PROJECT_BASE_DIR - Static variable in class ch.epfl.biop.qupath.utils.GUIUtils

R

RNAScopeCounts2 - Class in ch.epfl.biop.qupath.analysis

RNA Scope Counts in Fluorescence or Brightfield

RNAScopeCounts2() - Constructor for class ch.epfl.biop.qupath.analysis.RNAScopeCounts2

RoiSetLoader - Class in ch.epfl.biop.qupath.atlas.allen.utils

RoiSetLoader() - Constructor for class ch.epfl.biop.qupath.atlas.allen.utils.RoiSetLoader

run() - Method in class ch.epfl.biop.qupath.atlas.allen.commands.LoadAtlasRoisToQuPathCommand

run() - Method in class ch.epfl.biop.qupath.commands.ApplyDisplaySettingsCommand

run() - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

This is where the work happens We add the whole image annotation if needed and run the macroRunner We then remove the whole image annotation if we need it

runMacro(ParameterList, ImageData<BufferedImage>, ImageDisplay, PathObject, String) - Static method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

runPlugin(PluginRunner<BufferedImage>, String) - Method in class ch.epfl.biop.qupath.analysis.RNAScopeCounts2

runPlugin(PluginRunner<BufferedImage>, String) - Method in class ch.epfl.biop.qupath.utils.internal.ImageJMacroRunner

S

ScriptableMacroRunner - Class in ch.epfl.biop.qupath.utils

This is a wrapper around the MacroRunner to make it easier to script

ScriptableMacroRunner() - Constructor for class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

A Simple public class that must do a few things 1.

sendResultsToFile(ArrayList<String>, ArrayList<PathObject>) - Static method in class ch.epfl.biop.qupath.utils.Utils

sendResultsToFile(ArrayList<String>, ArrayList<PathObject>, File) - Static method in class ch.epfl.biop.qupath.utils.Utils

By making use of ObservableMeasurementTableData, we can query each result and get a string back Works, for area, pathclasses, parents, and of course any other measurement in the final table

sendResultsToFile(ArrayList<PathObject>) - Static method in class ch.epfl.biop.qupath.utils.Utils

setClearObjects(boolean) - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

setDownsample(int) - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

setGetOverlay(boolean) - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

setGetOverlayAs(String) - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

setGetROI(boolean) - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

setParameters(ParameterList) - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

setPathObject(PathObject) - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

setSendOverlay(boolean) - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

setSendROI(boolean) - Method in class ch.epfl.biop.qupath.utils.ScriptableMacroRunner

splitObject(PathObject, PathObject) - Static method in class ch.epfl.biop.qupath.utils.PathUtils

Splits the defined pathobject using the provided splitter.

st_level - Variable in class ch.epfl.biop.atlas.allen.AllenOntologyJson.AllenBrainRegion

U

um - Static variable in class ch.epfl.biop.qupath.utils.Utils

Utils - Class in ch.epfl.biop.qupath.utils

Utilities for QuPath scripting that make no use of the GUI

Utils() - Constructor for class ch.epfl.biop.qupath.utils.Utils

W

writeRegions(List<AllenOntologyJson.AllenBrainRegion>, int) - Static method in class ch.epfl.biop.atlas.allen.AllenOntologyJson

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