Index

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

A

addParameter(String) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Generic means of adding a cellpose parameter

addParameter(String, String) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Generic means of adding a cellpose parameter

B

batchSize(Integer) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Defines the batch size for training

build() - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Create a Cellpose2D, all ready for detection.

build() - Method in class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

Build a OpCreators.TileOpCreator according to the builder's parameters.

builder(File) - Static method in class qupath.ext.biop.cellpose.Cellpose2D

Load a previously serialized builder.

builder(String) - Static method in class qupath.ext.biop.cellpose.Cellpose2D

Create a builder to customize detection parameters.

C

cellConstrainScale - Variable in class qupath.ext.biop.cellpose.Cellpose2D

cellConstrainScale(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Constrain any cell expansion defined using CellposeBuilder.cellExpansion(double) based upon the nucleus size.

cellExpansion - Variable in class qupath.ext.biop.cellpose.Cellpose2D

cellExpansion(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Amount by which to expand detected nuclei to approximate the cell area.

Cellpose2D - Class in qupath.ext.biop.cellpose

Dense object detection based on the cellpose and omnipose publications

Cellpose2D() - Constructor for class qupath.ext.biop.cellpose.Cellpose2D

Cellpose2D.LogParser - Enum Class in qupath.ext.biop.cellpose

CellposeBuilder - Class in qupath.ext.biop.cellpose

Cell detection based on the following method:

CellposeBuilder(File) - Constructor for class qupath.ext.biop.cellpose.CellposeBuilder

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

CellposeBuilder(String) - Constructor for class qupath.ext.biop.cellpose.CellposeBuilder

Build a cellpose model by providing a string which can be the name of a pretrained model or a path to a custom model

cellposeChannels(Integer, Integer) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Explicitly set the cellpose channels manually.

CellposeExtension - Class in qupath.ext.biop.cellpose

Install Cellpose as an extension.

CellposeExtension() - Constructor for class qupath.ext.biop.cellpose.CellposeExtension

CellposeResultListener - Class in qupath.ext.biop.cellpose

CellposeResultListener() - Constructor for class qupath.ext.biop.cellpose.CellposeResultListener

cellposeSetup - Variable in class qupath.ext.biop.cellpose.Cellpose2D

CellposeSetup - Class in qupath.ext.biop.cellpose

CellposeSetup() - Constructor for class qupath.ext.biop.cellpose.CellposeSetup

cellprobThreshold(Double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

/** cellprob threshold, default is 0, decrease to find more and larger masks

channels(int...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Specify channels.

channels(String...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Specify channels by name.

channels(ColorTransforms.ColorTransform...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Define the channels (or color transformers) to apply to the input image.

classify(String) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Request that a classification is applied to all created objects.

classify(PathClass) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Request that a classification is applied to all created objects.

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

compartments - Variable in class qupath.ext.biop.cellpose.Cellpose2D

compartments(ObjectMeasurements.Compartments...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Specify the compartments within which intensity measurements are made.

compute(Mat) - Method in class qupath.ext.biop.cellpose.OpCreators.PercentileTileOpCreator

compute(Mat) - Method in class qupath.ext.biop.cellpose.OpCreators.ZeroMeanVarianceTileOpCreator

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

constrainToParent - Variable in class qupath.ext.biop.cellpose.Cellpose2D

constrainToParent(boolean) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

If true, constrain nuclei and cells to any parent annotation (default is true).

CP2 - Enum constant in enum class qupath.ext.biop.cellpose.Cellpose2D.LogParser

CP3 - Enum constant in enum class qupath.ext.biop.cellpose.Cellpose2D.LogParser

createAnnotations() - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Create annotations rather than detections (the default).

createOps(ImageDataOp, ImageData<BufferedImage>, ROI, ImagePlane) - Method in class qupath.ext.biop.cellpose.OpCreators.ZeroMeanVarianceTileOpCreator

createOps(ImageDataOp, ImageData<BufferedImage>, ROI, ImagePlane) - Method in interface qupath.ext.biop.cellpose.OpCreators.TileOpCreator

Compute the (tile-based) ops from the image.

creatorFun - Variable in class qupath.ext.biop.cellpose.Cellpose2D

D

detectObjects(ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.ext.biop.cellpose.Cellpose2D

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

detectObjectsImpl(ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.ext.biop.cellpose.Cellpose2D

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

diameter(Double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

The estimated diameter of the objects to detect.

doReadResultsAsynchronously - Variable in class qupath.ext.biop.cellpose.Cellpose2D

downsample(double) - Method in class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

Specify the downsample factor to use when calculating the normalization.

E

epochs(Integer) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Defines the number of epochs for training

eps(double) - Method in class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

Error constant used for numerical stability and avoid dividing by zero.

excludeEdges() - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Exclude on edges.

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

extendChannelOp - Variable in class qupath.ext.biop.cellpose.Cellpose2D

extendChannelOp(ImageOp) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

F

flowThreshold(Double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Flow error threshold, 0 turns off this optional QC step.

G

getCellposePythonPath() - Method in class qupath.ext.biop.cellpose.CellposeSetup

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

getCondaPath() - Method in class qupath.ext.biop.cellpose.CellposeSetup

getDescription() - Method in class qupath.ext.biop.cellpose.CellposeExtension

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

getInstance() - Static method in class qupath.ext.biop.cellpose.CellposeSetup

getName() - Method in enum class qupath.ext.biop.cellpose.Cellpose2D.LogParser

getName() - Method in class qupath.ext.biop.cellpose.CellposeExtension

getOmniposePythonPath() - Method in class qupath.ext.biop.cellpose.CellposeSetup

getOutputLog() - Method in class qupath.ext.biop.cellpose.Cellpose2D

Returns the log from running the cellpose command, with any error messages and status updates of the cellpose process You can use this during training or prediction

getPattern() - Method in enum class qupath.ext.biop.cellpose.Cellpose2D.LogParser

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.cellpose.Cellpose2D

Get the results table associated with the Quality Control run

getQuPathVersion() - Method in class qupath.ext.biop.cellpose.CellposeExtension

getRepository() - Method in class qupath.ext.biop.cellpose.CellposeExtension

getTrainingDirectory() - Method in class qupath.ext.biop.cellpose.Cellpose2D

The directory that was used for saving the training images

getTrainingResults() - Method in class qupath.ext.biop.cellpose.Cellpose2D

Returns a parsed version of the cellpose log as a ResultsTable with columns Epoch, Time, Loss, Loss Test and LR

getValidationDirectory() - Method in class qupath.ext.biop.cellpose.Cellpose2D

The directory that was used for saving the validation images

globalPathClass - Variable in class qupath.ext.biop.cellpose.Cellpose2D

globalPreprocess - Variable in class qupath.ext.biop.cellpose.Cellpose2D

groundTruthDirectory - Variable in class qupath.ext.biop.cellpose.Cellpose2D

groundTruthDirectory(File) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Specify the training directory

I

ignoreCellOverlaps - Variable in class qupath.ext.biop.cellpose.Cellpose2D

ignoreCellOverlaps(boolean) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

If true, ignore overlaps when computing cell expansion.

imageNormalizationBuilder() - Static method in class qupath.ext.biop.cellpose.Cellpose2D

Build a normalization op that can be based upon the entire (2D) image, rather than only local tiles.

imageNormalizationBuilder() - Static method in class qupath.ext.biop.cellpose.OpCreators

Build a normalization op that can be based upon the entire (2D) image, rather than only local tiles.

ImageNormalizationBuilder() - Constructor for class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

inputAdd(double...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Add an offset as a preprocessing step.

inputScale(double...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Multiply by a scale factor as a preprocessing step.

inputSubtract(double...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Subtract an offset as a preprocessing step.

installExtension(QuPathGUI) - Method in class qupath.ext.biop.cellpose.CellposeExtension

L

learningRate(Double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Defines the learning rate

M

maskThreshold(Double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Deprecated.

use CellposeBuilder.cellprobThreshold(Double)

maxDimension(int) - Method in class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

The maximum width or height, which is used to calculate a downsample factor for the image if OpCreators.ImageNormalizationBuilder.downsample(double) is not specified.

measureIntensity() - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Request default intensity measurements are made for all available cell compartments.

measureIntensity(Collection<ObjectMeasurements.Measurements>) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Request specified intensity measurements are made for all available cell compartments.

measurements - Variable in class qupath.ext.biop.cellpose.Cellpose2D

measureShape - Variable in class qupath.ext.biop.cellpose.Cellpose2D

measureShape() - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Request shape measurements are made for the detected cell or nucleus.

minTrainMasks(Integer) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Excludes training data with less than n training masks (n labels)

model - Variable in class qupath.ext.biop.cellpose.Cellpose2D

modelDirectory - Variable in class qupath.ext.biop.cellpose.Cellpose2D

modelDirectory(File) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Define the directory where the newly trained model should be saved

N

noCellposeNormalization() - Method in class qupath.ext.biop.cellpose.CellposeBuilder

convenience method? to deactivate cellpose normalization.

normalizePercentiles(double, double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Apply percentile normalization separately to the input image channels.

normalizePercentiles(double, double, boolean, double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Apply percentile normalization to the input image channels, or across all channels jointly.

normalizePercentilesGlobal(double, double, double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Convenience method to call global normalization for the dataset

nThreads - Variable in class qupath.ext.biop.cellpose.Cellpose2D

nThreads(int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Specify the number of threads to use for processing.

O

OMNI - Enum constant in enum class qupath.ext.biop.cellpose.Cellpose2D.LogParser

op - Variable in class qupath.ext.biop.cellpose.Cellpose2D

OpCreators - Class in qupath.ext.biop.cellpose

Helper class for creating new ImageOps based upon other image properties.

OpCreators() - Constructor for class qupath.ext.biop.cellpose.OpCreators

OpCreators.ImageNormalizationBuilder - Class in qupath.ext.biop.cellpose

Builder for a OpCreators.TileOpCreator that can be used for image preprocessing using min/max percentiles or zero-mean-unit-variance normalization.

OpCreators.PercentileTileOpCreator - Class in qupath.ext.biop.cellpose

Tile op creator that computes offset and scale values across the full image to normalize using min and max percentiles.

OpCreators.TileOpCreator - Interface in qupath.ext.biop.cellpose

Helper class for creating (tile-based) ImageOps with parameters that are derived from an entire image or ROI.

OpCreators.ZeroMeanVarianceTileOpCreator - Class in qupath.ext.biop.cellpose

Tile op creator that computes offset and scale values across the full image to normalize to zero mean and unit variance.

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

outputModelName - Variable in class qupath.ext.biop.cellpose.Cellpose2D

overlap - Variable in class qupath.ext.biop.cellpose.Cellpose2D

P

parameters - Variable in class qupath.ext.biop.cellpose.Cellpose2D

percentiles(double, double) - Method in class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

Specify min and max percentiles to calculate normalization values.

perChannel(boolean) - Method in class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

Compute the normalization values separately per channel; if false, values are computed jointly across channels.

pixelSize - Variable in class qupath.ext.biop.cellpose.Cellpose2D

pixelSize(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Resolution at which the cell detection should be run.

preprocess - Variable in class qupath.ext.biop.cellpose.Cellpose2D

preprocess(OpCreators.TileOpCreator) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Add an OpCreators.TileOpCreator to generate preprocessing operations based upon the entire image, rather than per tile.

preprocess(ImageOp...) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Add preprocessing operations, if required.

Q

qupath.ext.biop.cellpose - package qupath.ext.biop.cellpose

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

R

readResultsAsynchronously() - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Use an asynchronous method to read the results from the cellpose as it writes files Can result in faster processing.

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.cellpose.CellposeBuilder

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

saveTrainingImages() - Method in class qupath.ext.biop.cellpose.Cellpose2D

Goes through the current project and saves the images and masks 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'.

setCellposePythonPath(String) - Method in class qupath.ext.biop.cellpose.CellposeSetup

setCondaPath(String) - Method in class qupath.ext.biop.cellpose.CellposeSetup

setOmniposePythonPath(String) - Method in class qupath.ext.biop.cellpose.CellposeSetup

setOutputModelName(String) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Set the final model name.

setOverlap(int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Set the overlap (in pixels) between tiles.

showTrainingGraph() - Method in class qupath.ext.biop.cellpose.Cellpose2D

Overloaded method for backwards compatibility.

showTrainingGraph(boolean, boolean) - Method in class qupath.ext.biop.cellpose.Cellpose2D

Displays a JavaFX graph as a dialog, so you can inspect the Losses per epoch also saves the graph to the QC folder if requested

simplify(double) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Customize the extent to which contours are simplified.

simplifyDistance - Variable in class qupath.ext.biop.cellpose.Cellpose2D

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

T

tempDirectory(File) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Specify the temporary directory

tileHeight - Variable in class qupath.ext.biop.cellpose.Cellpose2D

tileSize(int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Size in pixels of a tile used for detection.

tileSize(int, int) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Size in pixels of a tile used for detection.

tileWidth - Variable in class qupath.ext.biop.cellpose.Cellpose2D

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

train() - Method in class qupath.ext.biop.cellpose.Cellpose2D

Executes the cellpose training by 1.

U

useGPU - Variable in class qupath.ext.biop.cellpose.Cellpose2D

useGPU(boolean) - Method in class qupath.ext.biop.cellpose.CellposeBuilder

overwrite use GPU

useMask(boolean) - Method in class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

Optionally use any ROI mask provided for the calculation.

useOmnipose() - Method in class qupath.ext.biop.cellpose.CellposeBuilder

Use Omnipose implementation: Adds --omni flag to command

V

valueOf(String) - Static method in enum class qupath.ext.biop.cellpose.Cellpose2D.LogParser

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

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.cellpose.Cellpose2D.LogParser

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

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

zeroMeanUnitVariance() - Method in class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

Normalize for zero mean and unit variance.

zeroMeanUnitVariance(boolean) - Method in class qupath.ext.biop.cellpose.OpCreators.ImageNormalizationBuilder

Optionally normalize for zero mean and unit variance.

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