GitHub topics: imagej

Repositories

jpsacha/sbt-imagej

sbt-imagej is an SBT (Simmple Build Tool) plugin that that helps with development of ImageJ plugins

Language: Scala - Size: 229 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 6 - Forks: 1

MontpellierRessourcesImagerie/imagej_macros_and_scripts

ImageJ macros and scripts written at the imaging facility MRI

Language: Jupyter Notebook - Size: 17.2 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 35 - Forks: 18

flika-org/flika

An interactive image processing program for biologists written in Python.

Language: Python - Size: 18.2 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 23 - Forks: 1

nicost/micro-manager Fork of micro-manager/micro-manager

Microscope control and image acquisition integrated with ImageJ.

Language: Java - Size: 289 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 16 - Forks: 11

scenerygraphics/sciview

sciview is a tool for visualization and interaction with ND image and mesh data

Language: Java - Size: 15.3 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 72 - Forks: 20

UU-cellbiology/ZstackDepthColorCode

Z-stack Depth Colorcode ImageJ FIJI plugin

Language: Java - Size: 58.6 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 24 - Forks: 7

morphonets/SNT Fork of fiji/SNT

The ImageJ framework for quantification of neuronal anatomy

Language: Java - Size: 45.6 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 52 - Forks: 19

mianalysis/mia

Modular, object-based analysis for ImageJ/Fiji

Language: Java - Size: 220 MB - Last synced at: 3 days ago - Pushed at: 10 days ago - Stars: 16 - Forks: 2

cgohlke/tifffile

Read and write TIFF files.

Language: Python - Size: 1.71 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 625 - Forks: 162

qupath/qupath

QuPath - Open-source bioimage analysis for research

Language: Java - Size: 96.4 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 1,196 - Forks: 310

cgohlke/roifile

Read and write ImageJ ROI format.

Language: Python - Size: 244 KB - Last synced at: about 11 hours ago - Pushed at: 4 months ago - Stars: 74 - Forks: 7

imjoy-team/imagej.js

ImageJS--Image analysis in the browser with ImageJ

Language: JavaScript - Size: 92.4 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 100 - Forks: 10

fmeyenhofer/NanoZoomer-J

ImageJ plugin for handling NDPI files.

Language: Java - Size: 29.3 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 1 - Forks: 0

UU-cellbiology/PTU_Reader

ImageJ plugin reading PicoQuant ptu/pt3 FLIM image files

Language: Java - Size: 221 KB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 7 - Forks: 1

imcf/imcf-fiji-scripts

:wrench: :memo: :coffee: :microscope: Scripts for Fiji provided by the Imaging Core Facility, Biozentrum, University of Basel

Language: Python - Size: 348 KB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 1 - Forks: 3

hallvaaw/awesome-biological-image-analysis

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

Size: 455 KB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 154 - Forks: 26

ToledoEM/Bash-blind-rename

Rename files on folder for manual image blind analysis to avoid bias.

Language: Swift - Size: 5.07 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 1 - Forks: 0

imagej/napari-imagej

Use ImageJ functionality from napari

Language: Python - Size: 3.97 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 31 - Forks: 5

AFMiJ/AFMiJ

Plugins to read and eleborate AFM data in ImageJ

Size: 46 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0

smith6jt-cop/KINTSUGI

Jupyter notebook based multiplex image processing pipeline.

Language: Jupyter Notebook - Size: 534 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 0

mbalatsko/opencv-rolling-ball

Fully Ported to Python from ImageJ's Background Subtractor. Rolling ball and sliding paraboloid background subtraction algorithms.

Language: Python - Size: 1.7 MB - Last synced at: 7 days ago - Pushed at: about 3 years ago - Stars: 48 - Forks: 7

bonej-org/BoneJ2

Plugins for bone image analysis

Language: Java - Size: 4.12 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 23 - Forks: 12

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 at: 12 days ago - Pushed at: 4 months ago - Stars: 7 - Forks: 3

imagingbook/imagingbook-public

Image processing software for textbooks by W. Burger & M. Burge

Language: Java - Size: 80.5 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 19 - Forks: 8

ijtools/ijGeometry

Geometry library for ImageJ/Fiji

Language: Java - Size: 277 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

BiologyTools/BioCore

Bio Library in .NET8. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Language: C# - Size: 107 MB - Last synced at: 16 days ago - Pushed at: 2 months ago - Stars: 4 - Forks: 1

ijpb/MorphoLibJ

Collection of mathematical morphology methods and plugins for ImageJ

Language: Java - Size: 26.4 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 106 - Forks: 48

GReD-Clermont/omero_batch-plugin Fork of brau-frederic/mica_omero

Language: Java - Size: 2.38 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 1

A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supports XInput game controllers to move stage, take images, run ImageJ macros on images or Bio C# scripts.

Language: C# - Size: 72.9 MB - Last synced at: 5 days ago - Pushed at: 3 months ago - Stars: 18 - Forks: 6

BiologyTools/BioGTK

A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Language: C# - Size: 146 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 14 - Forks: 2

BiologyTools/BioLib

A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions.

Language: C# - Size: 65.3 MB - Last synced at: 16 days ago - Pushed at: 3 months ago - Stars: 4 - Forks: 1

kwolbachia/Imagej-macro-addiction

"ça y est j'ai une idée! non deux, trois, oh lala, oh lala j'ai plein d'idées..."

Language: ImageJ Macro - Size: 2.47 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 1

gtatters/ThermImageJ

ImageJ functions and macros for working with thermal image files

Language: ImageJ Macro - Size: 18.4 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 52 - Forks: 6

BiologyTools/Bio

A .NET library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

Language: C# - Size: 28.9 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0

Samadarshi-Maity/Parallelized_ImageJ_wrapper

ImageJ Wrapper for heavily parallelized image processing. Allows memory allocation and multi processing options by instantiating the wrapper in every worker.

Language: Jupyter Notebook - Size: 322 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

ai4life-opencalls/oc_1_project_3

Ai4Life Open Call #1 - Project #3, semantic segmentation of kidney and heart tissue

Language: Jupyter Notebook - Size: 18.8 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Image-Py/imagepy

Image process framework based on plugin like imagej, it is esay to glue with scipy.ndimage, scikit-image, opencv, simpleitk, mayavi...and any libraries based on numpy

Language: Python - Size: 6.28 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 1,322 - Forks: 332

thorstenwagner/ij-ridgedetection

Detect ridges / lines with imagej

Language: Java - Size: 261 KB - Last synced at: 8 days ago - Pushed at: over 6 years ago - Stars: 44 - Forks: 28

anchoranalysis/anchor

Core libraries for Anchor - excluding plugins and projects.

Language: Java - Size: 27.1 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

lukmuk/em-scalebartools

Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image.

Language: ImageJ Macro - Size: 60 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 12 - Forks: 1

j-pyl/exo-2-clr

Detection and analysis pipeline of exocytosis in two-channel microscopy with FIJI and R

Language: ImageJ Macro - Size: 2.78 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

temshil/mri

Python and ImageJ Macro scripts to pre-process, analyze, and visualize MRI data.

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

jrijn/FijiTools

FijiTools2020 is a collection of tools designed for use in ImageJ/Fiji. The code was written for the analysis of microscopy images in the lab of Mikael Sellin, Uppsala University. Some of the scripts are meant to work in conjunction with a separately performed Trackmate analysis.

Language: Python - Size: 3.11 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

ropensci/ijtiff

An R Package for general purpose TIFF file I/O which plays nice with ImageJ

Language: R - Size: 58.1 MB - Last synced at: 4 days ago - Pushed at: 5 months ago - Stars: 17 - Forks: 9

tferr/Scripts

:microscope::cocktail: Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ

Language: Java - Size: 9.49 MB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 25 - Forks: 18

Rocsg/FijiRelax

FijiRelax: 3D+t multi-echo spin-echo sequences MRI analysis

Language: Java - Size: 7.76 MB - Last synced at: 4 days ago - Pushed at: 5 months ago - Stars: 8 - Forks: 4

BiologyTools/ImageJ.NET

ImageJ Control using C# and IKVM.

Size: 3.65 MB - Last synced at: 16 days ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 3

DylanMuir/ReadImageJROI

Matlab function to import ROIs from ImageJ

Language: MATLAB - Size: 8.79 KB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 27 - Forks: 6

UU-cellbiology/Correlescence

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

Language: Java - Size: 612 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 0

quantixed/CellMigration

Analysis of cell migration in Igor Pro

Language: IGOR Pro - Size: 3.94 MB - Last synced at: 3 days ago - Pushed at: about 4 years ago - Stars: 8 - Forks: 5

miura/Yodosha-BIASBook2025

『型で実践する生物画像解析　ImageJ・Python・napari』サポートサイト

Language: Jupyter Notebook - Size: 51.1 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

mattiaghilardi/MorFishJ

A software package for fish traditional morphometric analysis from side view images

Language: ImageJ Macro - Size: 582 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

vms10/rayleigh_method_natural_structures

Implementation of the Rayleigh method to study the optical response of natural photonic structures using digitalized images as an input.

Language: Python - Size: 96.8 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

areaDetector/ADViewers

ImageJ, Python, and IDL viewers for areaDetector detectors and cameras

Language: IDL - Size: 45.8 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 3 - Forks: 8

ijtools/ijDigiShapes

Generate synthetic images of geometric shapes within ImageJ

Language: Java - Size: 459 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

HMS-IAC/fiji-workshop

Materials supporting the ImageJ/Fiji workshop at Harvard Medical School.

Size: 628 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 2

zhousong99/CyberedgeImage

C# Image Processing. 支持多种图像格式如jpeg,png,dicom,tiff. 支持roi操作，支持各种滤波和增强

Language: C# - Size: 4.34 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

imcf/imcf-fiji-toolbars

:coffee: :microscope: :symbols: Fiji Action Bars provided by the IMCF.

Language: ImageJ Macro - Size: 173 KB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

quantixed/imagej-macros

quantixed FIJI update site

Language: ImageJ Macro - Size: 13.9 MB - Last synced at: 6 months ago - Pushed at: 8 months ago - Stars: 16 - Forks: 2

kwolbachia/KTZ-LUTs

Handmade ImageJ / Fiji LUTs for microscopy, scientific good visualization and art.

Size: 4.11 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 9 - Forks: 0

emx77/ASI_MTF

Imagej macro to calculate the MTF based on a knife edge measurement

Language: ImageJ Macro - Size: 924 KB - Last synced at: 4 months ago - Pushed at: 8 months ago - Stars: 17 - Forks: 4

ij-plugins/ijp-DeBayer2SX

Raw Bayer pattern to color image converters

Language: Scala - Size: 3.18 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 3

aleskl/imagej

A collection of customised ImageJ macros

Language: ImageJ Macro - Size: 50.8 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

cadaws/MaSCOT-AI

Mammary cell shape computation over time with Trackmate-Cellpose

Language: Python - Size: 5.31 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

knime-ip/knip

KNIME Image Processing Extension

Language: Java - Size: 212 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 50 - Forks: 11

thorstenwagner/ij-blob

ImageJ library to detect and analyse connected components (blobs) in binary images

Language: Java - Size: 176 KB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 3

Dahie/imageflow

Visual ImageJ Macro editing in a node-base editor featuring ImageJ

Language: Java - Size: 13.7 MB - Last synced at: 4 months ago - Pushed at: over 5 years ago - Stars: 18 - Forks: 4

imagingbook/imagingbook-calibrate

Java/ImageJ implementation of Zhang's camera calibration method

Language: Java - Size: 91.4 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 18 - Forks: 5

NicolasCristini/ImageJ-Processing-Assistant-Notebook

I.P.A.N. consist of a series of ready-to-use Jupyter Notebooks for performing image analysis. It includes a tutorial about the use of PyimageJ and a demonstration of image processing and data acquisition & visualisation.

Language: Jupyter Notebook - Size: 50.1 MB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

Wada-H/FRETratioFx

ImageJ plugin for creating FRET ratio

Language: Java - Size: 42 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

ij-plugins/ijp-color

Plugins for ImageJ - color space conversions and color calibration

Language: Scala - Size: 3.06 MB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 2

thorstenwagner/ij-nl-means

Non local means filter for ImageJ

Language: Java - Size: 174 KB - Last synced at: 8 days ago - Pushed at: almost 8 years ago - Stars: 12 - Forks: 7

CellDynamics/QuimP

QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.

Language: Java - Size: 36.2 MB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 7 - Forks: 2

ij-plugins/ijp-toolkit

ijp-toolkit general purpose plugins for ImageJ (also known as ij-plugins_toolkit)

Language: Java - Size: 30.5 MB - Last synced at: 5 months ago - Pushed at: 12 months ago - Stars: 16 - Forks: 3

ij-plugins/ijp-scala-console

Console for running Scala scripts.

Language: Scala - Size: 7.52 MB - Last synced at: about 1 month ago - Pushed at: 12 months ago - Stars: 3 - Forks: 2

jbstphr/ImageJ_GroundTruth_Brush

ImageJ: binary regions (semi-transparent imageROI-brush and/or fully-transparent shapeROI-brush)

Language: Java - Size: 1.16 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

konung-yaropolk/ImageJ-csv-cutter

Simple tool for Calcium-imaging data preprocessing, based on timing-metadata from Olympus Fluoview sowtware

Language: Python - Size: 117 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

borge-holme/celltraxx_download

Automated tracking of cell migration in phase contrast microscope images

Language: C - Size: 23.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

bockp/Edge-Detection-project

Tiny Image in Javascript - Edge Detection Algorithms

Language: JavaScript - Size: 13 MB - Last synced at: 2 months ago - Pushed at: over 7 years ago - Stars: 35 - Forks: 9

KeesStraatman/Random-points

Create random points in binary image and calculate number of points in objects of interest and distance to object of interest

Language: ImageJ Macro - Size: 9.77 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

MontpellierRessourcesImagerie/napari-J

Connect Napari with FIJI/ImageJ

Language: Python - Size: 130 KB - Last synced at: 18 days ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 2

Turku-BioImaging/ColonyArea

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

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

Jumitti/skeletonanalyzer

Python script to facilitate the processing of data obtained with the AnalyzeSkeleton tool from Fiji/ImageJ

Language: Python - Size: 4.88 KB - Last synced at: 2 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

amphybio/endomicroscopy-analysis

A unified non-supervised framework for characterizing colorectal cancer using endomicroscopic images

Language: Python - Size: 13.2 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

shermanlo77/oxwasp_phd

Code for the PhD thesis. The topic was on defect detection of 3D printing using x-rays. The repository includes an implementation of the mode filter and empirical null filter.

Language: TeX - Size: 7.6 MB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

swharden/PrairieView-Quick-Loader

ImageJ plugin to quickly load multiphoton imaging data from PrairieView folders

Language: Java - Size: 66.4 KB - Last synced at: 6 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

Scaramir/HD_colocalization

Preprocess, noise-reduction, threshold & quantify images to get box plots for each class (mainly cell cultures of different cel llines). Colocalization due to a naive trick of counting all overlapping signals/pixels. Could be done in ImageJ as well, but i thought this is better suited than fiddling with macros.

Language: Python - Size: 883 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0