Modifier and Type | Class and Description |
---|---|
class |
ChannelProvider
|
class |
ChannelProviderBinary
Implementation of
ChannelProvider that calls two ChannelProvider s that
must provide Channel s of the same dimensions. |
class |
ChannelProviderTernary
Implementation of
ChannelProvider that calls three ChannelProvider s that
must provide Channel s of the same dimensions. |
class |
ChannelProviderUnary
Implementation of
ChannelProvider that calls a single delegate ChannelProvider . |
class |
MaskProvider
|
class |
MaskProviderUnary
Implementation of
MaskProvider that calls a single delegate MaskProvider . |
Modifier and Type | Class and Description |
---|---|
class |
Arrange
Creates a stack that combines other stacks.
|
class |
StackProvider
|
class |
StackProviderUnary
Implementation of
StackProvider that calls a single delegate Provider<Stack> . |
Modifier and Type | Class and Description |
---|---|
class |
TileWithLabels
Tiles a number of
StackProviderWithLabel s as a single StackProvider . |
class |
WriteText
Creates an image that contains text only.
|
Modifier and Type | Class and Description |
---|---|
class |
AnisotropicDiffusion
Performs Perona-Malik Anisotropic
Diffusion.
|
class |
MinimumFilter |
Modifier and Type | Class and Description |
---|---|
class |
DistanceTransform3D
Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
|
class |
DistanceTransformForEachObject3D
Like
DistanceTransform3D but applies the distance transform separately for each object in
a collection. |
Modifier and Type | Class and Description |
---|---|
class |
AutoLocalThreshold
Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
|
Modifier and Type | Class and Description |
---|---|
class |
CreateNew
Creates a new channel with all values initialized to a constant (by default zero)
|
class |
Duplicate |
class |
FromDimensionsBase |
class |
FromInput
Finds the input-stack using a conventional name of
input_image - and extracts the first
channel |
class |
FromStack
Extracts a channel from a provider of a stack
|
class |
IfParamEquals |
class |
Reference |
class |
TwoVoxelMappingBase
Takes the two channels and creates a NEW third channel whose pixels are a function of the two
channels
|
class |
UnaryWithObjectsBase |
class |
UnaryWithValueBase
A
ChannelProviderUnary which has a scalar value field |
Modifier and Type | Class and Description |
---|---|
class |
AddConstant |
class |
ArithmeticWithConstantBase
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a
constant.
|
class |
ArithmeticWithConstantConditionallyWriteBase |
class |
Invert
Subtracts each voxel from the maximum value for the channel's data type (e.g.
|
class |
MaxTwoChannels |
class |
MaxWithConstant |
class |
MeanThreeChannels
Creates a new channel that is the mean of three input channels
|
class |
MinTwoChannels |
class |
MinWithConstant |
class |
MultiplyConstant |
class |
MultiplyTwoChannels |
class |
SubtractFromConstant |
class |
SubtractMean
Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
|
class |
SubtractTwoChannels |
Modifier and Type | Class and Description |
---|---|
class |
AssignFromChannel
Copies the pixels from
channelAssignFrom to channel (possibly masking) |
class |
AssignFromDictionary |
class |
AssignFromIntersectingObjects
Matches source-objects to target objects, based upon intersection, and assigns the value in the
respective source object to the target object
|
class |
AssignValue
Assigns a constant (scalar) value to the portion of the image covered by a mask
|
Modifier and Type | Class and Description |
---|---|
class |
Convert<T>
Converts a channel by applying a converter (no histogram is involved in the conversion).
|
class |
ConvertBase |
class |
ConvertWithHistogram<T>
Converts a channel to a different voxel data-type by applying a converter with an associated
histogram.
|
Modifier and Type | Class and Description |
---|---|
class |
GradientBase
Base class to calculate the gradient of the voxels in a
Channel . |
class |
GradientBaseAddSum
Like
GradientBase but allows an arbitrary constant to be added to voxels storing the
gradient. |
class |
GradientForAxis
Extracts the gradient in the direction of a particular axis (identified by an index)
|
class |
GradientXY
Calculates a
Channel 's gradient along the x and y axes. |
class |
Sobel
3x3 Sobel Filter
|
Modifier and Type | Class and Description |
---|---|
class |
Blur
Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
|
class |
IfVoxelZero
Creates a new channel which is a merged version of two input channels according to rules.
|
class |
Median
Applies a median-filter with square kernel
|
class |
NormalizeDifferenceToMedian
Corrects a channel in the following way
|
class |
NormalizeObjectIntensity
Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
|
class |
QuantileStretch
Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel
data range
|
class |
ScaleXY
Scales the channel in the X and Y dimensions.
|
Modifier and Type | Class and Description |
---|---|
class |
FromMask |
class |
FromMaskBase
A base class for a
ChannelProvider which also uses a binary-mask, but which doesn't use
any other ChannelProvider as an input. |
class |
UnaryWithMaskBase |
class |
ZeroOutsideMask
Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
|
Modifier and Type | Class and Description |
---|---|
class |
LevelPerObjectBase
Creates a channel with a level calculated for each object variously
|
class |
LevelPerObjectIndependently
Creates a channel with different threshold-levels for each object, calculating the level only
from the histogram of the particular object.
|
class |
LevelPerObjectNeighbors
Calculates a threshold-level for each object collectively based on other objects
|
Modifier and Type | Class and Description |
---|---|
class |
IdentifyObjects
Assigns a unique id number to each object.
|
class |
ScoreObjects |
class |
ScoreVoxels
Assigns a score (a value indicating how probable something is) to each voxel
|
Modifier and Type | Class and Description |
---|---|
class |
ExtractCenterSlice
Extracts the slice at the center (rounding down) of the range of z-stacks.
|
class |
ExtractSliceRange
Extracts slices from
sliceStart (inclusive) to sliceEnd (inclusive). |
class |
MaximumIntensityProjection |
class |
MeanIntensityProjection |
class |
RepeatSlice
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an
existing channel
|
Modifier and Type | Class and Description |
---|---|
class |
AllValuesOff
Creates a new mask of particular dimensionality where all values are off.
|
class |
AllValuesOn
Creates a new mask of particular dimensionality where all values are on.
|
class |
FromChannelBase
Base-class for
MaskProvider s that accept a Channel as input. |
Modifier and Type | Class and Description |
---|---|
class |
And
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the
result.
|
class |
CombineBase |
class |
IfHighLow
Outputs the logical operation
iff first==HIGH and second==LOW then LOW voxelwise on both
masks, modifying {mask} with the result. |
class |
Or
Outputs the logical operation or voxelwise on both masks, modifying {mask} with the
result.
|
class |
Xor
Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask}
with the result.
|
Modifier and Type | Class and Description |
---|---|
class |
FromChannel
Creates a mask from an existing channel, reusing the channel's buffer and considering all 0
values as off, and 255 values as on.
|
class |
FromObjects
Creates a
Mask from a collection of object-masks. |
class |
FromStackChannel |
Modifier and Type | Class and Description |
---|---|
class |
Box
Creates a
Mask where all pixels are on within a box region. |
class |
Dilate
Performs a dilation morphological operation on
BinaryVoxels . |
class |
Erode
Performs an erosion morphological operation on
BinaryVoxels . |
class |
ExteriorContour
Finds the exterior outer contour for a
Mask that forms its outline. |
class |
FitBoxToOnVoxels
Fits a box around the on voxels.
|
class |
MorphologicalOperatorBase
Base class for performing morphological operations on
BinaryVoxels . |
Modifier and Type | Class and Description |
---|---|
class |
IfKeyValueCondition
The current
mask is returned if a condition on key-values is satisfied otherwise maskElse is returned. |
class |
IfNotEmpty
The current
mask is returned if it's non-empty (at least one on voxel) otherwise
maskElse is returned. |
class |
IfObjectFilter
The current
mask is returned if the mask (treated as an object) passed an object-filter,
otherwise maskElse is returned. |
class |
IfPredicateBase
Base class which multiplexes between the current mask and an alternative depending if a condition
is met.
|
class |
IfStackExists
The current
mask is a particular stack exists (at least one on voxel) otherwise
maskElse is returned. |
Modifier and Type | Class and Description |
---|---|
class |
SegmentChannel
Applies a
BinarySegmentation algorithm to derive a mask from a channel |
class |
Threshold
Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel
if possible.
|
Modifier and Type | Class and Description |
---|---|
class |
FlattenZ
Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity
projection).
|
Modifier and Type | Class and Description |
---|---|
class |
Concatenate
Combines all the channels from one or more sources (stacks, channels etc.)
|
class |
FromChannelOrMask
Creates a stack from a channel or mask (reusing the voxel buffers)
|
Modifier and Type | Class and Description |
---|---|
class |
ColoredBase
Base class for providers that draw entities (an outline or filled) on a background
|
class |
ColoredBaseWithGenerator
Like
ColoredBase but uses a generator to determine the colors for the objects |
class |
ColoredMask
Draws a colored representation (outline or filled) of a
ObjectMask on a background |
class |
ColoredObjects
Draws a colored representation (outline or filled) of an
ObjectCollection on a background |
class |
ThreeChannels |
class |
ThreeColoredObjects
Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
|
Modifier and Type | Class and Description |
---|---|
class |
BackgroundSubtractor |
class |
WithFilterBase |
class |
WithRadiusBase
A
ChannelProviderUnary with a 'radius' parameter |
Modifier and Type | Class and Description |
---|---|
class |
EdgeFilterIJ |
class |
GaussianBlur2D |
Modifier and Type | Class and Description |
---|---|
class |
MeanFilter2D |
class |
VarianceFilter2D |
Modifier and Type | Class and Description |
---|---|
class |
MedianFilter2D |
class |
MedianFilter3D |
Modifier and Type | Class and Description |
---|---|
class |
FillHoles |
class |
MorphologicalOperation
Applies an ImageJ (2D) morphological operation to each slice
|
Modifier and Type | Class and Description |
---|---|
class |
MontageSlices |
Modifier and Type | Class and Description |
---|---|
class |
ColoredMarks
Draws a colored representation (outline or filled) of an
MarkCollection on a background |
Modifier and Type | Class and Description |
---|---|
class |
ColorConverterBase
Converts a RGB stack into another color space using OpenCV.
|
class |
ConvertRGBToHSV
Converts a RGB image to the HSV color
space.
|
class |
ConvertRGBToLab
Converts a RGB image to the Lab color
space.
|
Modifier and Type | Class and Description |
---|---|
class |
ConvexHull2D
Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
|
class |
ConvexHull3D |
class |
ConvexHullBase |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.