mianalysis/mia

Modular, object-based analysis for ImageJ/Fiji

Language: Java - Size: 217 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 11 - Forks: 2

trackmate-sc/TrackMate

TrackMate is your buddy for your everyday tracking.

Language: Java - Size: 11.9 MB - Last synced: 4 days ago - Pushed: 6 days ago - Stars: 148 - Forks: 73

saalfeldlab/n5-ij

ImageJ convenience layer for N5

Language: Java - Size: 2.63 MB - Last synced: 10 days ago - Pushed: 12 days ago - Stars: 13 - Forks: 8

MultimodalImagingCenter/MIC-MAQ

MIC-MAQ for Microscopy Images of Cells - Multi Analyses and Quantifications is an ImageJ/Fiji Plugin for automatic segmentation of nuclei and/or cells for quantifications in other channels including foci detection

Language: Java - Size: 12.6 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

bonej-org/BoneJ2

Plugins for bone image analysis

Language: Java - Size: 4.18 MB - Last synced: 8 days ago - Pushed: 12 days ago - Stars: 19 - Forks: 12

UU-cellbiology/KymoResliceWide

ImageJ plugin making kymographs of maximum or average intensity with wide lines, polylines, curves

Language: Java - Size: 154 KB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 4 - Forks: 1

ekatrukha/UnequalTiffs

making montage or combine tiff images of different sizes

Language: Java - Size: 131 KB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 0 - Forks: 0

sankeert1999/Virtual-Orientation-Tools-VOTj

Virtual Orientation Tool FIJI (VOTj) : A Fiji plugin for object centering and alignment

Language: Python - Size: 41 MB - Last synced: 24 days ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

ekatrukha/BigTrace

FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets

Language: Java - Size: 3.06 MB - Last synced: 25 days ago - Pushed: 26 days ago - Stars: 21 - Forks: 2

MAILFERT-Sebastien/UNLOC

[ImageJ] Single Molecule Localization Microscopy (SMLM) plugin: UNLOC

Size: 306 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

DIDSR/BoneJ_Headless

Scripts for executing Fiji plugin BoneJ in headless mode in Python to compute bone microstructure metrics

Language: Python - Size: 396 MB - Last synced: 24 days ago - Pushed: 6 months ago - Stars: 4 - Forks: 2

joda01/evanalyzer

EV analyzing plugin for Fiji

Language: Java - Size: 316 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 4 - Forks: 0

UU-cellbiology/bvv-playground

playing with BigVolumeViewer LUTs/gamma/render

Language: Java - Size: 1.56 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 0

UU-cellbiology/ZstackDepthColorCode

Z-stack Depth Colorcode ImageJ FIJI plugin

Language: Java - Size: 56.6 KB - Last synced: 4 days ago - Pushed: over 3 years ago - Stars: 21 - Forks: 6

lmb-freiburg/Unet-Segmentation

The U-Net Segmentation plugin for Fiji (ImageJ)

Language: Java - Size: 2.1 MB - Last synced: 16 days ago - Pushed: over 1 year ago - Stars: 86 - Forks: 25

yu-lab-vt/SynQuant

A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images.

Language: Java - Size: 21.7 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 11 - Forks: 4

h39s/VessCoopJ

ImageJ Plugin for Automated Cancer Cell Vessel Co-option Analysis

Language: Java - Size: 8.79 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

antinos/T-SNE-ImageJ

An ImageJ/Fiji port of Leif Jonsson's pure Java t-SNE (https://github.com/lejon/T-SNE-Java)

Language: Java - Size: 52 MB - Last synced: 5 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

nxsaken/whiplugin

Wound Healing Assay Plugin for FIJI/ImageJ

Language: Java - Size: 388 KB - Last synced: 5 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

UniBoDS4H/IA

Fiji / ImageJ plugin for Imaging Alignment. This plugin manages two types of alignment: Manual Alignment and Automatic Alignment.

Language: Java - Size: 100 MB - Last synced: about 1 month ago - Pushed: 8 months ago - Stars: 8 - Forks: 0

thorstenwagner/ij-nanotrackj

NanoTrackJ is an ImageJ/Fiji plugin to characterize the size of nanoparticles by its diffusion trajectories.

Language: Java - Size: 51.8 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 2 - Forks: 1

fiji/pQCT

Fiji plugins for pQCT image analysis.

Language: Java - Size: 712 KB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 5

Chlanda-Lab/cryoCLEM

Toolbox for post-correlation cryo-CLEM workflow developed at Chlanda Lab, Heidelberg University.

Language: Java - Size: 103 KB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0

CellMoTher/AccPbFRET

An ImageJ plugin for analysis of acceptor photobleaching FRET images :electric_plug:

Language: Java - Size: 201 KB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

L-EL/TreeJ

Fiji/ImageJ plugin to annotate a labeled image

Language: Java - Size: 70.9 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 0

ishibaki/awesome-imagej-plugins

😎 Awesome lists about ImageJ Plugins!

Size: 21.5 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

UU-cellbiology/ComDet

ImageJ plugin detecting and colocalizing particles of given size (vesicles, dots, etc on biological microscopy images)

Language: Java - Size: 1.77 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 13 - Forks: 4

LauLauThom/Fiji-QualiAnnotations

Fiji plugins for qualitative image annotations + analysis workflows for image-classification and data-visualization

Language: Python - Size: 5.61 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 1

hansenjn/NuclQ

NuclQ - an ImageJ plugin to quantify intensity levels by distance to the nuclear membrane.

Language: Java - Size: 106 KB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

UU-cellbiology/DoM_Utrecht

Detection of Molecules plugin for ImageJ, Utrecht University

Language: Java - Size: 8.67 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 12 - Forks: 4

ComplexOrganizationOfLivingMatter/Fiji-plugins

GitHub Repository which is used as a Maven Repository

Size: 24.2 MB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

ekatrukha/CurveTrace

Curve tracing ImageJ plugin

Language: Java - Size: 934 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 13 - Forks: 3

goehringlab/saibr_fiji_plugin

A simple GUI-based FIJI plugin for performing spectral autofluorescence correction on biological images

Language: Java - Size: 177 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 2 - Forks: 0

UU-cellbiology/Correlescence

spatial and temporal cross correlations in 1D and 2D for fluorescent microscopy (ImageJ plugin)

Language: Java - Size: 612 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 0

ariel-waisman/LabelsToROIs

A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification

Language: Python - Size: 2.02 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 17 - Forks: 8

acayuelalopez/CellTypeAnalyzer

:microscope: This is an ImageJ or Fiji plugin to identify, characterize, quantify and classify cells according to user-defined conditions.

Language: Java - Size: 103 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 4 - Forks: 0

CellMoTher/RiFRET

An ImageJ plugin for intensity-based three-filter set (ratiometric) FRET :electric_plug:

Language: Java - Size: 457 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

theresaswayne/stereology

ImageJ scripts for stereology and morphometry

Language: Python - Size: 6.84 KB - Last synced: 6 months ago - Pushed: almost 7 years ago - Stars: 4 - Forks: 0

UU-cellbiology/PTU_Reader

ImageJ plugin reading PicoQuant ptu/pt3 FLIM image files

Language: Java - Size: 206 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 5 - Forks: 1

hadim/maskflow 📦

Maskflow: Object Detection and Segmentation for Cell Biology.

Language: Jupyter Notebook - Size: 23.8 MB - Last synced: 28 days ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

tferr/ASA 📦

Legacy project, now part of https://github.com/morphonets/SNT. Bitmap morphometry of neuronal arbors through Sholl

Language: Java - Size: 2.45 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 5

Turku-BioImaging/ColonyArea

ImageJ-plugin that is optimized to perform standard analysis of colony formation assays conducted in 6- to 24-well dishes.

Language: ImageJ Macro - Size: 13.1 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

bruvellu/WormBox

Fiji/ImageJ plugin to help measuring linear distances.

Language: Python - Size: 1.59 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

pmascalchi/ImageJ_AutoClickerJ

A plugin to combine power of mouse and keyboard control with image processing and analysis tools in ImageJ

Size: 51.8 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 4 - Forks: 0

arttumiettinen/fast-thickmap-imagej

Fast local thickness map plugin for ImageJ/Fiji

Language: Java - Size: 4.39 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 3 - Forks: 0

phflot/variational_aligner_IJ

ImageJ and Fiji Plugin for fast, variational 1D alignment of multichannel linescan data

Language: Java - Size: 1.3 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

xulman-obsoleteProjects/image-net-transfers-java

Java implementation of a proprietary image transfer protocol

Language: Java - Size: 1.3 MB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

hansenjn/ExtractSharpestPlane_JNH

ExtractSharpestPlane_JNH is an ImageJ/FIJI plugin to automatically extract the sharpest plane by highest SD from image stacks for large data sets.

Language: Java - Size: 56.6 KB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

sedflix/Active-Contours-API-for-Fiji-ImageJ

This is an easy to use active contours api for Fiji(ImageJ).

Language: Java - Size: 2.93 KB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 2 - Forks: 0

sedflix/EmbryoSegmentation

An ImageJ PlugIn for cell segmentation in an embryo of c.elegans

Language: Java - Size: 84 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 2

sufyanshk/imagej

ImageJ macros and plugins.

Language: Rich Text Format - Size: 9.77 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

thorstenwagner/ij-trajectory-classifier

This plugin segments and classify diffusion trajectories

Language: Java - Size: 47 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 3 - Forks: 3

ComputationalIntelligenceGroup/MaxLoGs

Maximum of Laplacian of Gaussian filters (imageJ plugin)

Language: Java - Size: 28.3 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

pmascalchi/ImageJ_WorkflowJ

WorkflowJ, a new plugin to create and save workflows in ImageJ / Fiji

Size: 13.7 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

ComputationalIntelligenceGroup/ObjCounter

ObjCounter ImageJ plugin for object segmentation and counting

Language: Java - Size: 442 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 2

MichaelWrana/MicroscopePlugins

Language: Java - Size: 21.5 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

thorstenwagner/ij-irregular-watershed

Watershed for irregular objects

Language: Java - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: almost 8 years ago - Stars: 0 - Forks: 0