Ecosystem

Below follows an non-exhaustive list of Fiji plugins and other software that uses either ImgLib2 or BigDataViewer:

 

PerkinElmer Operetta Importer

ImageJ
SciJava
Hold your horses

 

BVV-playground

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
Volume rendering of bdv datasets with gamma and transparency option

 

Multiview Reconstruction

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data.

 

SamJ

ImgLib2
SciJava
Segment Anything Model (SAM), and similar models, wrapper for Java based software.

 

SAM network inside Fiji

ImageJ
ImgLib2
SciJava
A Fiji plugin for interactive segmentation using the SAM network

 

metaseg

ImageJ
Fiji
BigDataViewer
ImgLib2
Meta-segmentation tool for joining many segmentation hypotheses created by various methods.

 

Deform

Fiji
BigDataViewer
ImgLib2
SciJava
Deform HDF5 sources

 

SNT

ImageJ
Fiji
ImgLib2
SciJava
The ImageJ framework for quantitative neuroanatomy

MoBIE

Fiji/ImageJ
BigDataViewer
imglib2
MoBIE is a Fiji plugin for exploring large multi-modal image data sets.

 

indago

ImageJ
Fiji
BigDataViewer
ImgLib2
indigare (ital.) - investigate.

 

Big Stitcher

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
Multiview stitching of large datasets.

 

Cosem-segmentation-analysis

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava

 

BigDataViewer Playground Display

ImageJ
Fiji
BigDataViewer
SciJava
Display (metadata and projectors) for BigDataViewer Playground.

 

BIGCAT

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
Collaborative volume annotation and segmentation with BigDataViewer

 

MoBIE IO

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
Readers and writers for image data in MoBIE projects

 

ImgLib2 Icy

ImgLib2
ImgLib2 wrappers for Icy sequences.

BigDataProcessor2

Fiji
ImageJ
BigDataViewer
HDF5
BigDataProcessor2 (BDP2) is a Fiji plugin for interactive processing of TB-sized image data.

 

Biop Bigdataviewer Tools and Plugins

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
Big data viewer tools BIOP - EPFL

 

PredictorOp

Fiji
BigDataViewer
ImgLib2
SciJava
Model runner demo for ImgLib2 consumers.

 

Selector For BigDataViewer

ImageJ
Fiji
BigDataViewer
SciJava
Selector Behaviours for BigDataViewer

 

Hot-knife

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava

 

FMI TrackMate Add-ons

ImageJ
Fiji
ImgLib2
SciJava
FMI Add-ons for TrackMate in Fiji

 

Paintera

Fiji
BigDataViewer
ImgLib2
SciJava
New Era Painting and annotation tool

 

BigDataViewer Bioformats Bridge

ImageJ
Fiji
BigDataViewer
SciJava
Commands and function for opening, conversion and easy use of bioformats format into BigDataViewer

BigTrace plugin

Fiji/ImageJ
BigDataViewer
imglib2
BigVolumeViewer
FIJI plugin for tracing and analysis of curvilinear structures (filaments, vessels, neurites) in volumetric microscopy datasets.

 

Imagejfx

ImageJ
Fiji
ImgLib2
SciJava

 

Fiji Plugin PlateViewer

Fiji
BigDataViewer
ImgLib2
SciJava
Fiji plugin for inspection of high-throughput microscopy multi-well image data

 

limeseg

ImageJ
ImgLib2
SciJava
Lipid Membrane Segmentation method for FIJI/ImageJ. https://doi.org/10.1186/s12859-018-2471-0

 

BigWarp plugin for Fiji

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
A tool for manual pointwise deformable registration using bigdataviewer.

Fiji

Fiji
ImageJ
BigDataViewer
ImgLib2
Fiji is an image processing package—a “batteries-included” distribution of ImageJ and ImageJ2, bundling a lot of plugins which facilitate scientific image analysis.

 

Fiji Plugin PlateViewer

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
TODO

 

Multiview Simulation

Fiji
ImgLib2
SciJava
Library for simulating a multi-view acquisition including attenuation, convolution, reduced sampling and poission noise.

 

Point manager for imglib2 and imagej projects

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
A tool for managing imglib2 RealPoints.

Labkit

Fiji
BigDataViewer
ImgLib2
Pixel Classification
Segmentation
Labkit is a user-friendly Fiji plugin for the segmentation of microscopy image data.

 

Keller Lab Block file type (.klb) - BigDataViewer backend

Fiji
BigDataViewer
SciJava
The KLB is a file format developed at the Keller Lab at Janelia Research Campus to efficiently store and retrieve large 5D images (>4GB) using lossless compression. The…

 

ilastik imageJ modules

ImageJ
ImgLib2
SciJava
These ImageJ plugins wrap ilastik workflows

 

Janelia Render Tools And Services

SciJava
A collection of tools and HTTP services (APIs) for rendering transformed image tiles.

 

MaMuT

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
Fiji plugin for the annotation of massive, multi-view data.

 

Plugin To Register Images to Atlases

ImageJ
Fiji
BigDataViewer
SciJava
Collection of tools to register images to atlases in Fiji.

 

plugins/CircleSkinner_.jar

ImageJ
ImgLib2
SciJava
A Fiji plugin for the automated detection and quantification of circular structure in images.

 

MoBIE Fiji Viewer

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
Fiji viewer for MoBIE projects

 

Phase Contrast Segmentation Toolbox (PHANTAST)

ImageJ
Fiji
ImgLib2
SciJava
The phae contrast segmentation toolbox (PHANTAST) enables high performance segmentation of phase contrast microscopy images

 

imglib2access

ImgLib2
Simplified access to ImgLib2 pixel data for teaching purposes

Mastodon

Fiji
ImageJ
BigDataViewer
ImgLib2
Mastodon is a large-scale tracking and track-editing framework for large, multi-view images.

 

MTrack

ImageJ
Fiji
ImgLib2
SciJava
MTrack

 

mars-swing

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
Swing GUI for analysis of single-molecule TIRF and FMT data in the Structure and Dynamics of Molecular Machines research group

 

Colocalization_by_Cross_Correlation

ImageJ
Fiji
ImgLib2
SciJava
An ImageJ plugin for spatial correlation/colocalization analysis that is more compatible with super-resolution images than traditional pixel-wise colocalization algorithms.…

 

ScanCo100_BoneJ_Calibration

ImageJ
Fiji
ImgLib2
SciJava
Plugin to import ScanCo100 bone density calibration from DICOM metadata. May work with similar metadata from other scanners, but this is untested. Available at ImageJ update…

 

InteractiveWatershed

ImageJ
ImgLib2
SciJava 
    InteractiveWatershed

 

mars-fx

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
JavaFX GUI for processing single-molecule TIRF and FMT data in the Structure and Dynamics of Molecular Machines research group.

 

mars-core

ImageJ
ImgLib2
SciJava
Molecule Archive Suite (Mars) - core data storage and processing algorithms.

 

Fiji plugin for context aware trainable segmentation

Fiji
BigDataViewer
ImgLib2
SciJava
A plugin for context aware trainable segmentation of big image data.

 

BIOP Kheops Command

ImageJ
Fiji
BigDataViewer
SciJava
IJ2 commands that use bio-formats to create pyramidal ome.tiff

 

Radial Symmetry

ImageJ
Fiji
BigDataViewer
ImgLib2
SciJava
A plugin for radial symmetry localization on smFISH (and other) images.

 

Spimdata Extra Settings

ImageJ
Fiji
BigDataViewer
SciJava
Repo containing extra settings that can be stored in spimdata file format

 

Label Editor

ImageJ
Fiji
BigDataViewer
SciJava
UI component for image segmentation label comparison and selection

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