A B C E F G H I L M N O P R S T U V W

A

About - Class in org.incenp.imagej.plugins

About() - Constructor for class org.incenp.imagej.plugins.About

actionPerformed(ActionEvent) - Method in class org.incenp.imagej.plugins.MergeDialog

actionPerformed(ActionEvent) - Method in class org.incenp.imagej.plugins.PanelDialog

apply(ImagePlus, String, String) - Method in class org.incenp.imagej.ChannelMasker

Apply this ChannelMasker object to an image.

apply(ImagePlus, String) - Method in class org.incenp.imagej.ChannelMasker

Apply this ChannelMasker object to an image.

applyMask(ImageProcessor, ImageProcessor, BinaryOperator, int) - Static method in class org.incenp.imagej.Masking

Apply a binary mask to another image.

applyMask(ImageProcessor, ImageProcessor) - Static method in class org.incenp.imagej.Masking

Apply a binary mask to another image by performing a AND operation.

applyMasker(ImagePlus, String, String, String) - Static method in class org.incenp.imagej.ChannelMasker

Apply a list of operations to an image.

augmentHyperstack(ImagePlus, int) - Static method in class org.incenp.imagej.Helper

Augments a hyperstack with empty channel(s).

B

BatchReader - Class in org.incenp.imagej

A class to open images from a CSV file containing filenames and optional associated data.

BatchReader(String, boolean) - Constructor for class org.incenp.imagej.BatchReader

Creates a new reader.

BatchReader(String) - Constructor for class org.incenp.imagej.BatchReader

Creates a new reader.

BatchReader(File) - Constructor for class org.incenp.imagej.BatchReader

Creates a new reader.

BatchReader(File, boolean) - Constructor for class org.incenp.imagej.BatchReader

Creates a new reader.

BinaryOperator - Enum in org.incenp.imagej

Binary operations that can be used when combining two images.

C

chain(ChannelMasker) - Method in class org.incenp.imagej.ChannelMasker

Sets a ChannelMasker to apply after the current one.

ChannelMasker - Class in org.incenp.imagej

A helper class to create and apply binary masks.

ChannelMasker(ChannelMasker.ChannelOperation[]) - Constructor for class org.incenp.imagej.ChannelMasker

Creates a new ChannelMasker object with the given list of operations.

close() - Method in class org.incenp.imagej.BatchReader

Closes any opened images.

CLOSE_OPEN_MASK - Static variable in class org.incenp.imagej.Masking

Performs a round of close/open operations when creating a mask.

countBlackPixels(ImageProcessor) - Static method in class org.incenp.imagej.Helper

Counts all black pixels in a given image.

countPixels(ImageProcessor) - Static method in class org.incenp.imagej.Helper

Counts all non-black pixels in a given image.

countPixels(ImageProcessor, int) - Static method in class org.incenp.imagej.Helper

Counts all pixels above the specified threshold.

countWhitePixels(ImageProcessor) - Static method in class org.incenp.imagej.Helper

Counts all white pixels in a given image.

createAugmentedHyperstack(ImagePlus, int, boolean) - Static method in class org.incenp.imagej.Helper

Creates a copy of a given hyperstack with added (empty) channel(s).

createMask(ImageProcessor, ThresholdingMethod, int, int) - Static method in class org.incenp.imagej.Masking

Creates a binary mask by thresholding a source image.

createMask(ImageProcessor, ThresholdingMethod, int) - Static method in class org.incenp.imagej.Masking

Create a binary mask by thresholding a source image.

createMasker(String, String, int) - Static method in class org.incenp.imagej.ChannelMasker

Creates a ChannelMasker from a text description of the operations.

createMasker(String, String) - Static method in class org.incenp.imagej.ChannelMasker

Creates a ChannelMasker object from a text description of the operations.

createMasker(String) - Static method in class org.incenp.imagej.ChannelMasker

Creates a ChannelMasker object from a text description of the operations.

E

ExtendedPanel - Class in org.incenp.imagej.plugins

ExtendedPanel() - Constructor for class org.incenp.imagej.plugins.ExtendedPanel

extractVolumes(ImagePlus, int[]) - Static method in class org.incenp.imagej.Helper

Extracts the volumes occupied by white pixels in a image.

extractVolumes(ImagePlus, boolean) - Static method in class org.incenp.imagej.Helper

Extracts the volumes occupied by white pixels in a image.

extractVolumes(ImagePlus) - Static method in class org.incenp.imagej.Helper

Extracts the volumes occupied by white pixels in a image.

F

fillResultsTable(ResultsTable) - Method in class org.incenp.imagej.BatchReader

Update a ResultsTable with the contents of the current row.

FrameIntervalInfo - Class in org.incenp.imagej.plugins

FrameIntervalInfo(ImagePlus) - Constructor for class org.incenp.imagej.plugins.FrameIntervalInfo

fromString(String) - Static method in enum org.incenp.imagej.BinaryOperator

fromString(String) - Static method in enum org.incenp.imagej.ThresholdingMethod

G

getCell(int) - Method in class org.incenp.imagej.BatchReader

Gets the contents of a specific cell within the current row.

getCell(String[], String) - Method in class org.incenp.imagej.BatchReader

Gets the contents of a specific cell within the current row.

getCell(String[]) - Method in class org.incenp.imagej.BatchReader

Gets the contents of a specific cell within the current row.

getCell(String) - Method in class org.incenp.imagej.BatchReader

Gets the contents of a specific cell within the current row.

getChannelOrder() - Method in class org.incenp.imagej.ChannelMasker

Gets the default channel order specification.

getCSVRow(char) - Method in class org.incenp.imagej.BatchReader

Gets the current row as a single string, with values separated by the specified character.

getCSVRow() - Method in class org.incenp.imagej.BatchReader

Gets the current row as a single string containing comma-separated values.

getHeaders() - Method in class org.incenp.imagej.BatchReader

Gets the headers as found in the CSV file.

getImage() - Method in class org.incenp.imagej.BatchReader

Gets the current image.

getMaskingOptions() - Method in class org.incenp.imagej.ChannelMasker

Gets the masking options currently used by this object.

getPackageInfo() - Static method in class org.incenp.imagej.plugins.Info

getResultsTable(String) - Static method in class org.incenp.imagej.Helper

Gets or creates a ResultsTable.

getRow() - Method in class org.incenp.imagej.BatchReader

Gets a copy of the current row.

getTimeAtFrame(int) - Method in class org.incenp.imagej.plugins.FrameIntervalInfo

getVersion() - Static method in class org.incenp.imagej.plugins.Info

H

hasImage() - Method in class org.incenp.imagej.BatchReader

Indicates if there’s an image ready to be processed.

hasInfo() - Method in class org.incenp.imagej.plugins.FrameIntervalInfo

Helper - Class in org.incenp.imagej

A class of static helper methods.

Helper() - Constructor for class org.incenp.imagej.Helper

I

Info - Class in org.incenp.imagej.plugins

Info() - Constructor for class org.incenp.imagej.plugins.Info

L

Launcher - Class in org.incenp.imagej.plugins

ImageJ launcher.

Launcher() - Constructor for class org.incenp.imagej.plugins.Launcher

M

main(String[]) - Static method in class org.incenp.imagej.plugins.Launcher

Masking - Class in org.incenp.imagej

A class of helper methods to create and manipulate binary masks.

Masking() - Constructor for class org.incenp.imagej.Masking

MergeDialog - Class in org.incenp.imagej.plugins

MergeDialog(MergeInfo) - Constructor for class org.incenp.imagej.plugins.MergeDialog

N

next() - Method in class org.incenp.imagej.BatchReader

Moves to the next available image.

NO_DUPLICATE - Static variable in class org.incenp.imagej.Masking

Avoid duplicating the source image when possible.

NucleiSegmenter - Class in org.incenp.imagej

This class provides methods implementing the Watershed segmentation of cell nuclei as described in https://imagej.net/Nuclei_Watershed_Separation.

NucleiSegmenter(double, AutoThresholder.Method) - Constructor for class org.incenp.imagej.NucleiSegmenter

Creates a new nuclei segmenter.

NucleiSegmenter(double) - Constructor for class org.incenp.imagej.NucleiSegmenter

Creates a new nuclei segmenter with the “Moments” thresholding algorithm.

O

org.incenp.imagej - package org.incenp.imagej

org.incenp.imagej.plugins - package org.incenp.imagej.plugins

P

PanelDialog - Class in org.incenp.imagej.plugins

PanelDialog(PanelInfo) - Constructor for class org.incenp.imagej.plugins.PanelDialog

R

readCSV() - Method in class org.incenp.imagej.BatchReader

Reads the entire CSV file.

run() - Method in class org.incenp.imagej.plugins.About

run() - Method in class org.incenp.imagej.plugins.ExtendedPanel

run() - Method in class org.incenp.imagej.plugins.UnifiedMerge

runDialog(MergeInfo) - Static method in class org.incenp.imagej.plugins.MergeDialog

runDialog(PanelInfo) - Static method in class org.incenp.imagej.plugins.PanelDialog

S

segment(ImageProcessor) - Method in class org.incenp.imagej.NucleiSegmenter

Segments a single image.

segment(ImagePlus, int[], int[], int[]) - Method in class org.incenp.imagej.NucleiSegmenter

Segments a hyperstack.

segment(ImagePlus, int[]) - Method in class org.incenp.imagej.NucleiSegmenter

Segments a hyperstack, including all slices and all frames.

segment(ImagePlus) - Method in class org.incenp.imagej.NucleiSegmenter

Segments an entire hyperstack.

setCaseSensitive(boolean) - Method in class org.incenp.imagej.BatchReader

Sets the case-sensitivity option.

setChannelOrder(String) - Method in class org.incenp.imagej.ChannelMasker

Sets the default channel order specification.

setInterval(int, int) - Method in class org.incenp.imagej.plugins.FrameIntervalInfo

setInterval(int, boolean) - Method in class org.incenp.imagej.plugins.FrameIntervalInfo

setMaskingOptions(int) - Method in class org.incenp.imagej.ChannelMasker

Sets the masking options used by this object.

stateChanged(ChangeEvent) - Method in class org.incenp.imagej.plugins.MergeDialog

stateChanged(ChangeEvent) - Method in class org.incenp.imagej.plugins.PanelDialog

T

ThresholdingMethod - Enum in org.incenp.imagej

Available thresholding methods.

toGlobalMethod() - Method in enum org.incenp.imagej.ThresholdingMethod

Translate this value to a AutoThresholder.Method value.

toLocalMethod() - Method in enum org.incenp.imagej.ThresholdingMethod

Translate this value to a string representation of a local thresholding algorithm.

U

UnifiedMerge - Class in org.incenp.imagej.plugins

UnifiedMerge() - Constructor for class org.incenp.imagej.plugins.UnifiedMerge

V

valueOf(String) - Static method in enum org.incenp.imagej.BinaryOperator

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

valueOf(String) - Static method in enum org.incenp.imagej.ThresholdingMethod

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

values() - Static method in enum org.incenp.imagej.BinaryOperator

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

values() - Static method in enum org.incenp.imagej.ThresholdingMethod

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

W

WHITE_MASK - Static variable in class org.incenp.imagej.Masking

Treats white pixels are masked.

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