Index

A B C D E G H I L M N O P Q R S T V Z
All Classes and Interfaces|All Packages

A

addParameter(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Generic means of adding a spotiflow parameter

addParameter(String, String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Generic means of adding a spotiflow parameter

B

build() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Create a Spotiflow, all ready for detection.

builder() - Static method in class qupath.ext.biop.spotiflow.Spotiflow

Create a builder to customize detection parameters.

builder(File) - Static method in class qupath.ext.biop.spotiflow.Spotiflow

Load a previously serialized builder.

C

channels - Variable in class qupath.ext.biop.spotiflow.Spotiflow

channels(int...) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Specify channels.

channels(String...) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Specify channels by name.

channelsIdx - Variable in class qupath.ext.biop.spotiflow.Spotiflow

classChannelName - Variable in class qupath.ext.biop.spotiflow.Spotiflow

cleanTempDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow

cleanTempDir() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

clear all files in the temp directory

cleanTrainingDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow

cleanTrainingDir() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

clear all files in the training directories

clearAllChildObjects - Variable in class qupath.ext.biop.spotiflow.Spotiflow

clearAllChildObjects() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Remove all child objects (i.e.

clearChildObjectsBelongingToCurrentChannels - Variable in class qupath.ext.biop.spotiflow.Spotiflow

clearChildObjectsBelongingToCurrentChannels() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Remove child objects (i.e.

closeWatchService() - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner

CONDA - Enum constant in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType

createAnnotations() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Create annotations rather than detections (the default).

creatorFun - Variable in class qupath.ext.biop.spotiflow.Spotiflow

D

detectObjects(ImageData<BufferedImage>, String, Collection<? extends PathObject>) - Method in class qupath.ext.biop.spotiflow.Spotiflow

Detect cells within one or more parent objects, firing update events upon completion.

disableGPU - Variable in class qupath.ext.biop.spotiflow.Spotiflow

disableGPU() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Forces using CPU instead of GPU

doNotApplyDataAugmentation - Variable in class qupath.ext.biop.spotiflow.Spotiflow

doNotApplyDataAugmentation() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Force to not apply data augmentation on images during the training

doSubpixel - Variable in class qupath.ext.biop.spotiflow.Spotiflow

doSubpixel(boolean) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Allows to go subpixel resolution

E

EXE - Enum constant in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType

G

getChangedFiles() - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner

getCondaPath() - Method in class qupath.ext.biop.spotiflow.SpotiflowSetup

getDescription() - Method in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType

getDescription() - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension

getExtensionVersion() - Static method in class qupath.ext.biop.spotiflow.SpotiflowExtension

getInstance() - Static method in class qupath.ext.biop.spotiflow.SpotiflowSetup

getName() - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension

getProcess() - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner

getProcessLog() - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner

getQCResults() - Method in class qupath.ext.biop.spotiflow.Spotiflow

Get the results table associated with the Quality Control run

getQuPathVersion() - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension

getRepository() - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension

getSpotiflowPythonPath() - Method in class qupath.ext.biop.spotiflow.SpotiflowSetup

H

helpPredict() - Method in class qupath.ext.biop.spotiflow.Spotiflow

Prints the help and the available CLI arguments for the prediction command

helpTrain() - Method in class qupath.ext.biop.spotiflow.Spotiflow

Prints the help and the available CLI arguments for the training command

I

includeNegatives - Variable in class qupath.ext.biop.spotiflow.Spotiflow

includeNegatives() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set the learning rate of the model for the training

installExtension(QuPathGUI) - Method in class qupath.ext.biop.spotiflow.SpotiflowExtension

isOmeZarr - Variable in class qupath.ext.biop.spotiflow.Spotiflow

L

lr - Variable in class qupath.ext.biop.spotiflow.Spotiflow

M

minDistance - Variable in class qupath.ext.biop.spotiflow.Spotiflow

modelDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow

modelToFineTune - Variable in class qupath.ext.biop.spotiflow.Spotiflow

N

nEpochs - Variable in class qupath.ext.biop.spotiflow.Spotiflow

nEpochs(int) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set the number of epochs for the training

nThreads - Variable in class qupath.ext.biop.spotiflow.Spotiflow

nThreads(int) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Specify the number of threads to use for processing.

O

OTHER - Enum constant in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType

P

parameters - Variable in class qupath.ext.biop.spotiflow.Spotiflow

pathClass - Variable in class qupath.ext.biop.spotiflow.Spotiflow

pointClasses - Variable in class qupath.ext.biop.spotiflow.Spotiflow

pretrainedModelName - Variable in class qupath.ext.biop.spotiflow.Spotiflow

probabilityThreshold - Variable in class qupath.ext.biop.spotiflow.Spotiflow

process3d - Variable in class qupath.ext.biop.spotiflow.Spotiflow

process3d() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Allows to process all slices of 3D stack.

process3d(boolean) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Deprecated.

use SpotiflowBuilder.process3d() instead

Q

qupath.ext.biop.cmd - package qupath.ext.biop.cmd

qupath.ext.biop.spotiflow - package qupath.ext.biop.spotiflow

R

runCommand(boolean) - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner

This builds, runs the command and outputs it to the logger as it is being run

S

saveBuilder(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Save this builder as a JSON file in order to be able to reuse it in place

savePredictionImages(boolean) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Deprecated.

use SpotiflowBuilder.cleanTempDir() instead

saveTempImagesAsOmeZarr() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

True to save images in the temp folder as OME-Zarr files.

saveTrainingImages() - Method in class qupath.ext.biop.spotiflow.Spotiflow

Goes through the current project and saves the images and point coordinates to the training and validation directories

setArguments(List<String>) - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner

This is the code you actually want to run after 'python'.

setClass(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Allows to go subpixel resolution

setClassChannelName() - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Allows to go subpixel resolution

setCondaPath(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowSetup

setLearningRate(double) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set the learning rate of the model for the training

setMinDistance(double) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set minimum distance between spots for NMS

setModelDir(File) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set model directory to use for prediction

setModelToFineTune(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set the name of the pre-trained model to fine-tune

setPointClass(String...) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Specify the class(es) of point to use for the training.

setPretrainedModelName(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set pre-trained model to use for prediction

setProbabilityThreshold(double) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set probability threshold for peak detection

setSpotiflowPythonPath(String) - Method in class qupath.ext.biop.spotiflow.SpotiflowSetup

setTrainingOutputDir(File) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set output folder to save a new model

setupChannels(ImageData<BufferedImage>, Integer[]) - Method in class qupath.ext.biop.spotiflow.Spotiflow

Get the name of the channels from their index and fill a map<ChannelName, ChannelIndex>

Spotiflow - Class in qupath.ext.biop.spotiflow

Spot detection based on the following method:

Spotiflow() - Constructor for class qupath.ext.biop.spotiflow.Spotiflow

SpotiflowBuilder - Class in qupath.ext.biop.spotiflow

Spot detection based on the following method:

SpotiflowBuilder() - Constructor for class qupath.ext.biop.spotiflow.SpotiflowBuilder

Build a spotiflow model

SpotiflowBuilder(File) - Constructor for class qupath.ext.biop.spotiflow.SpotiflowBuilder

can create a spotiflow builder from a serialized JSON version of this builder.

SpotiflowExtension - Class in qupath.ext.biop.spotiflow

Install Spotiflow as an extension.

SpotiflowExtension() - Constructor for class qupath.ext.biop.spotiflow.SpotiflowExtension

spotiflowSetup - Variable in class qupath.ext.biop.spotiflow.Spotiflow

SpotiflowSetup - Class in qupath.ext.biop.spotiflow

SpotiflowSetup() - Constructor for class qupath.ext.biop.spotiflow.SpotiflowSetup

startWatchService(Path) - Method in class qupath.ext.biop.cmd.VirtualEnvironmentRunner

T

tempDirectory - Variable in class qupath.ext.biop.spotiflow.Spotiflow

tempDirectory(File) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set input folder to predict spots

testDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow

toString() - Method in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType

train() - Method in class qupath.ext.biop.spotiflow.Spotiflow

Executes the spotiflow training by 1.

trainingInputDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow

trainingOutputDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow

V

validationInputDir - Variable in class qupath.ext.biop.spotiflow.Spotiflow

valueOf(String) - Static method in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType

Returns the enum constant of this class with the specified name.

values() - Static method in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType

Returns an array containing the constants of this enum class, in the order they are declared.

VENV - Enum constant in enum class qupath.ext.biop.cmd.VirtualEnvironmentRunner.EnvType

VirtualEnvironmentRunner - Class in qupath.ext.biop.cmd

A wrapper to run python virtualenvs, that tries to figure out the commands to run based on the environment type

VirtualEnvironmentRunner(String, VirtualEnvironmentRunner.EnvType, String) - Constructor for class qupath.ext.biop.cmd.VirtualEnvironmentRunner

VirtualEnvironmentRunner(String, VirtualEnvironmentRunner.EnvType, String, String) - Constructor for class qupath.ext.biop.cmd.VirtualEnvironmentRunner

VirtualEnvironmentRunner.EnvType - Enum Class in qupath.ext.biop.cmd

This enum helps us figure out the type of virtualenv.

Z

zEnd - Variable in class qupath.ext.biop.spotiflow.Spotiflow

zPositions(int, int) - Method in class qupath.ext.biop.spotiflow.SpotiflowBuilder

Set a substack for 3D training / prediction.

zStart - Variable in class qupath.ext.biop.spotiflow.Spotiflow

A B C D E G H I L M N O P Q R S T V Z
All Classes and Interfaces|All Packages