All Classes and Interfaces
Class
Description
Fiji menu entry for "Analyze Alignment Errors".
Sortable results browser for
AnalyzeErrorsUtil.Controls when row clicks recentre BDV.
Aggregated error statistics for one (groupA, groupB) bucket.
Display mode for
AnalyzeErrorsResultsWindow.Per-(viewA, viewB) error result returned by
AnalyzeErrorsUtil.getErrors(net.preibisch.mvrecon.fiji.spimdata.SpimData2, java.util.List<mpicbg.spim.data.sequence.ViewId>, java.util.Map<java.lang.String, java.lang.Double>).Bundle of dialog choices returned by
AnalyzeErrorsUtil.getParametersExtended(net.preibisch.mvrecon.fiji.spimdata.SpimData2, java.util.List<mpicbg.spim.data.sequence.ViewId>).Per-group aggregate of errors and connected groups (Single-view mode, grouped).
Per-view aggregate of errors and connections (Single-view mode, ungrouped).
A four-element axis angle represented by double-precision floating point
x,y,z,angle components.
A four-element axis angle represented by single-precision floating point
x,y,z,angle components.
Shared category-colour utilities for explorer-driven BDV highlights.
Source-name utilities used by both
BDVPopup (eager) and
LazyBDVPopup so they label sources identically as
"VS: <viewSetupId> TP: <timepointId>".Utility methods for BigDataViewer operations.
RealRandomAccess that computed cosine-blending for a certain interval
This BlockGenerator cares that the overlap within the image is accounted for and that
an outofbounds strategy is taken into account.
This BlockGenerator only cares that the overlap within the image is accounted for, not about
an outofbounds strategy.
We need to sort blocks in a way so consecutive ones are not influenced by their predecessors
Center of mass GUI
Center of Mass (Avg/Median) implementation
Holds flattened coefficient array and dimensions.
A three-element color value represented by single precision floating point
x,y,z values.
Generate a stream of `random' saturated RGB colors with all colors being
maximally distinct from each other.
Executes one Lucy-Richardson iteration on one specifc block.
Executes one Lucy-Richardson iteration on one specifc block.
Executes one Lucy-Richardson iteration on one specifc block.
Criterion based on multi-consensus RANSAC sets.
Computes the content-based fusion on a given image
Utility methods for managing interest point correspondences.
Defines a pair of corresponding interest points
Criterion that counts cross-view corresponding interest points within a region.
Interface to load the native library for separable convolution using CUDA/CPU
(https://github.com/StephanPreibisch/SeparableConvolutionCUDALib)
Executes gaussian convolution using the native CUDA implementation
(https://github.com/StephanPreibisch/SeparableConvolutionCUDALib)
One view for the multiview deconvolution, contains image, weight, and PSFs
Handles the PSF for a specific view for the deconvolution
General class for LightSheetZ1 and MicroManager
DefineDataSet Parameters class
Visualizes the density at a certain location given the radius
Static helpers to persist displacement fields to an N5/Zarr container and
reload them as in-memory
ArrayImgs.Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation
and Linear Interpolation.
Computes the convolution of an image with an arbitrary kernel.
This model just applies some other
TranslationInvariantModel without computing anything.Compute the Fourier Ring Correlation, a measure of the resolution of a microscopy image.
Computes the fourier ring correlation at specific positions and interpolates between all points
Fast Redundant Geometric Local Descriptor Matching (RGLDM)
Interface for interactive parsing of spimdata XMLs
Class that actually computes the geometric hashing
Single interest point, extends InterestPoint to remember where it came from for grouping
Implementation of the ICP, takes anything RealLocalizable and internally uses LinkedInterestPoint to compute the ICP
Plugin to fuse images using transformations from the SpimData object
Plugin to fuse images using transformations from the SpimData object
Plugin to fuse images using transformations from the SpimData object
Integrating Nearest-neighbor search in an Euclidean space.
Plugin to detect interest points, store them on disk, and link them into the XML
Different plugins to detect interest points are supported, needs to implement the
InterestPointDetectionGUI interfaceSingle interest point, extends mpicbg Point by an id
Interface for grouping interest points from multiple views that are in one group
The simplest way to group interest points, just add them all (this will create problems in overlaps)
The simplest way to group interest points, just add them all (this will create problems in overlaps)
A list of interest points for a certain label, can save and load from textfile as specified in the XML
Serializable data container for interest points and correspondences.
The type Interest point tools.
Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation
and Linear Interpolation.
Iterative closest point implementation
Iterative closest point implementation
Landmarks (corresponding source and target coordinates) that can be used
to construct a
ThinplateSplineTransform.Convenience methods to create lazy evaluated cached cell images with ops or consumers.
BigStitcher Affine Fusion in blocks
Opt-in alternative to
BDVPopup that opens BigDataViewer with NO sources
and then dynamically adds (and removes / hides) sources as the user selects views
in the explorer.Simple Gaussian filter Op
Simple Gaussian filter Op
DataSet definition for LightSheetZ1
A double precision floating point 3 by 3 matrix.
A single precision floating point 3 by 3 matrix.
A double precision floating point 4 by 4 matrix.
A single precision floating point 4 by 4 matrix.
Uses the previous state as an approximate knowledge for the metadata of the acquisition.
DataSet definition for MicroManager
Mirrors an n-dimensional image along an axis (one of the dimensions).
Submenu for managing missing views: mark as missing, mark as present, or mark as missing with metadata removal.
This class does a simple matching but computes a normalizationFactor based a given model prior.
n-dimensional extension of the monotone cubic spline implementation by Leszek Wach:
https://gist.github.com/lecho/7627739#file-splineinterpolation-java
Adapted version from the MicroManager codebase that supports the new diSPIM related tags
and multiple-file reading.
Adapted version from the MicroManager codebase that supports the new diSPIM related tags
and multiple-file reading.
Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation
and Linear Interpolation.
Generic criterion interface for deciding whether to continue splitting
an octant in the oct-tree splitting algorithm.
Lightweight structure for correspondence data during splitting.
Tight overlap test for two affine-transformed voxel cubes (parallelepipeds in world space)
via the 3-D Separating Axis Theorem (SAT).
A 1D point.
A 3 element point that is represented by double precision floating point
x,y,z coordinates.
A 3 element point that is represented by single precision floating point
x,y,z coordinates.
A 3 element point represented by signed integer x,y,z coordinates.
A 4 element vector represented by double precision floating point x,y,z,w
coordinates.
A 4 element point represented by single precision floating point x,y,z,w
coordinates.
A match of two 1D points.
Fuse one portion of a paralell fusion, supports no weights
Fuse one portion of a paralell fusion, supports no weights
A 4-element quaternion represented by double precision floating point x,y,z,w
coordinates.
A 4 element unit quaternion represented by single precision floating point
x,y,z,w coordinates.
Simple utility to track retry attempts and handle retry logic for failed
blocks.
Redundant Geometric Local Descriptor Matching (RGLDM)
Tests whether the ROI was changed and will recompute the preview
AWS-SDK-touching S3 configuration, intentionally isolated from
URITools.Adjust brightness and colors for individual (or groups of)
setups and having a scrollpane if necessaryDialog for selecting views based on predefined ranges and values.
Indicates that inverse of a matrix can not be computed.
Extends the
SpimData class; has additonally detectionsA single nail landmark donated from one split sub-view's surface onto
the recipient underlying view's TPS.
One TPS landmark, classified by category.
Adaptive oct-tree based image splitting with recursive correspondence partitioning.
Result of a split operation, including intervals and statistics.
Base result of splitting a single view.
Callback for saving correspondences on-the-fly.
Callback for saving interest points (detections + correspondences) on-the-fly.
Result of processing a single ViewSetup's split intervals.
Interface for splitting views into sub-intervals.
A
RealRandomAccessible whose samples are generated by trivial
projection of the lower dimensional source
into a higher dimensional target by continuous
stacking, i.e. when projecting from 1D to 3D, the samples at
f(5) = g(5,2,3) = g(5,1,6) = g(5,18,-20)...Base StackList class for various kinds of DataSet definition class
DataSet definition for ImageJ
DataSet definition for LOCI
Created by moon on 7/2/15.
Interface to be implemented by classes that need access to the global stitching results
A generalized transform object represented internally as a 4x4
double-precision floating point matrix.
Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation
Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation
and Linear Interpolation.
Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation
and Linear Interpolation.
3d-affine transformation models to be applied to points in 3d-space.
This model just applies some other
TranslationInvariantModel without computing anything.This class is a subtle hint that
Models which are used to fit AbstractPointDescriptors should be translation invariant.2d-rigid transformation models to be applied to points in 2d-space.
3d-rigid transformation models to be applied to points in 3d-space.
3d-rigid transformation models to be applied to points in 3d-space.
A generic 3-element tuple that is represented by double-precision floating
point x,y,z coordinates.
A generic 3-element tuple that is represented by single precision-floating
point x,y,z coordinates.
A 3-element tuple represented by signed integer x,y,z coordinates.
A 4 element tuple represented by double precision floating point x,y,z,w
coordinates.
A 4-element tuple represented by single-precision floating point x,y,z,w
coordinates.
Compute the corrected intensity when
intensity was observed in a
pixel that has been bleached by previously being imaged.A 3-element vector that is represented by double-precision floating point
x,y,z coordinates.
A 3-element vector that is represented by single-precision floating point
x,y,z coordinates.
A 4-element vector represented by double-precision floating point x,y,z,w
coordinates.
A 4-element vector represented by single-precision floating point x,y,z,w
coordinates.
Maps from a String label to a list of interest points for a specific viewid
A class that organizes all interest point detections of all
ViewDescriptions (which extend ViewId)Reusable per-view neighbour queries:
ViewNeighbors.connectedViews(SpimData2, Collection, Map) — interest-point correspondence neighbours
ViewNeighbors.overlappingViews(SpimData2, Collection) — geometric (bounding-box) neighbours
Both restrict their results to the universe set passed in (typically the views the
caller is already analysing).Companion window of
FilteredAndGroupedExplorerPanel that highlights views in BDV which
are correspondence-connected to the explorer's current selection.Companion window of
FilteredAndGroupedExplorerPanel that highlights views in BDV which
geometrically overlap the explorer's current selection.Dummy class so we can use XmlIoFlatfieldCorrectedWrappedImgLoader for both
multiresolution and non-multiresolution ImgLoaders with flatfield correction