Topic: imagej Goto Github

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acayuelalopez / celltypeanalyzer
imagej,:microscope: This is an ImageJ or Fiji plugin to identify, characterize, quantify and classify cells according to user-defined conditions.
User: acayuelalopez
imagej fiji-plugin image-processing

ariel-waisman / labelstorois
imagej,A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification
User: ariel-waisman
cell-segmentation computer-vision fiji fiji-plugin image-analysis imagej label-images segmentation

biologytools / biogtk
imagej,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.
User: biologytools
Home Page: https://github.com/BiologyTools/BioGTK
bio-formats biology gtk image-stacks imagej microscopy roi cross-platform omero imagej-roi

biologytools / bioimager
imagej,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.
User: biologytools
Home Page: https://discord.com/channels/1075990609707417600/1075990610160394302
imaging microscopy image-stacks imagej scripting imagej-macro whole-slide-imaging microscope microscope-control microscope-stage-controller

bockp / edge-detection-project
imagej,Tiny Image in Javascript - Edge Detection Algorithms
User: bockp
Home Page: https://github.com/crazybiocomputing/times
imagej edge-detection-algorithms benchmark javascript webgl edge-detection laplace sobel algorithm canny-edge-detection

bonej-org / bonej2
imagej,Plugins for bone image analysis
Organization: bonej-org
fiji-plugin image-analysis image-processing imagej-plugins maven-multimodule java-8 imagej travis-ci scientific-computing skeletal-biology

bruvellu / color-blind-luts
imagej,Color blind friendly lookup tables for Fiji/ImageJ
User: bruvellu
fiji imagej lut lookup-tables colorblind-friendly colorblindness colorschemes

cgohlke / roifile
imagej,Read and write ImageJ ROI format
User: cgohlke
Home Page: https://pypi.org/project/roifile
python imagej format-reader region-of-interest

cgohlke / tifffile
imagej,Read and write TIFF files
User: cgohlke
Home Page: https://pypi.org/project/tifffile
python image tiff imagej ome-tiff numpy zarr whole-slide-imaging format-reader life-sciences-image

dahie / imageflow
imagej,Visual ImageJ Macro editing in a node-base editor featuring ImageJ
User: dahie
imagej java node-based-ui

dylanmuir / readimagejroi
imagej,Matlab function to import ROIs from ImageJ
User: dylanmuir
Home Page: http://dylan-muir.com/articles/read_ij_roi/
matlab imagej imagej2 import roi

emx77 / asi_mtf
imagej,Imagej macro to calculate the MTF based on a knife edge measurement
User: emx77
imagej-macro electron-microscopy image-analysis x-ray-imaging point-spread-function mtf imagej imagej-plugins

flika-org / flika
imagej,An interactive image processing program for biologists written in Python.
Organization: flika-org
Home Page: http://flika-org.github.io/
biologists python imagej calcium image-processing fluorescence microscopy neurons astrocytes

gtatters / thermimagej
imagej,ImageJ functions and macros for working with thermal image files
User: gtatters
heat-transfer temperature-reading thermal-imaging imagej-macro fiji-macro imagej fiji exiftool perl ffmpeg

hadim / maskflow-fiji
imagej,A Fiji plugin for object detection and tracking based on MaskRCNN.
User: hadim
neural-network segmentation imagej fiji tensorfow microscopy

hallvaaw / awesome-biological-image-analysis
imagej,A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
User: hallvaaw
biology imaging microscopy segmentation imagej cellprofiler image-analysis awesome awesome-list bioimage-analysis

ij-plugins / ijp-color
imagej,Plugins for ImageJ - color space conversions and color calibration
Organization: ij-plugins
ijp-color scala imagej sbt-imagej

ij-plugins / ijp-toolkit
imagej,ijp-toolkit general purpose plugins for ImageJ (also known as ij-plugins_toolkit)
Organization: ij-plugins
scala imagej sbt-imagej ijp-toolkit image-processing image-analysis texture-synthesis

ijpb / morpholibj
imagej,Collection of mathematical morphology methods and plugins for ImageJ
Organization: ijpb
Home Page: http://imagej.net/MorphoLibJ
image-processing image-analysis imagej fiji mathematical-morphology 3d-images morpholibj

image-py / imagepy
imagej,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
Organization: image-py
Home Page: http://imagepy.org
imagej opencv scikit-image simpleitk

imagej / napari-imagej
imagej,Use ImageJ functionality from napari
Organization: imagej
Home Page: https://napari-imagej.readthedocs.io
fiji imagej java napari python

imagingbook / imagingbook-calibrate
imagej,Java/ImageJ implementation of Zhang's camera calibration method
User: imagingbook
Home Page: http://www.imagingbook.com
camera-calibration imagej java burger-burge

imagingbook / imagingbook-common
imagej,Common Java library for digital image processing books by Burger & Burge (OBSOLETE!)
User: imagingbook
Home Page: http://www.imagingbook.com
digital-image-processing imagej imagingbook burger-burge

imagingbook / imagingbook-public
imagej,Image processing software for textbooks by W. Burger & M. Burge
User: imagingbook
burger-burge digital-image-processing imagej imagej-plugins imagingbook java

imjoy-team / imagej.js
imagej,ImageJS--Image analysis in the browser with ImageJ
Organization: imjoy-team
Home Page: https://ij.imjoy.io
imagej image-processing

ivangtorre / multifrac
imagej,This is a plugin for ImageJ2 for multifractal analysis of 2D and 3D images. Cite: MULTIFRAC: An ImageJ plugin for multiscale characterization of 2D and 3D stack images . IG Torre, R. J. Heck and AM Tarquis. SoftwareX, 12, 100574.
User: ivangtorre
Home Page: https://imagej.net/Multifrac
multifractal-analysis imagej-plugin imagej 3d-images java fractal multifractal

joachimgoedhart / quantify-intensity-from-timelapse
imagej,Step-by-step instruction to quantify fluorescence intensities from timelapse imaging experiments
User: joachimgoedhart
imagej fluorescence-intensity fluorescence-microscopy-imaging time-series-analysis

knime-ip / knip
imagej,KNIME Image Processing Extension
Organization: knime-ip
Home Page: https://www.knime.com/community/image-processing
knime java image processing analysis imagej imagej2 imglib2 fiji scijava integration

lukmuk / em-scalebartools
imagej,Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image.
User: lukmuk
imagej fiji electron-microscopy scalebar

mbalatsko / opencv-rolling-ball
imagej,Fully Ported to Python from ImageJ's Background Subtractor. Rolling ball and sliding paraboloid background subtraction algorithms.
User: mbalatsko
imagej python3 image-processing background-subtraction rolling-ball sliding-paraboloid

mianalysis / mia
imagej,Modular, object-based analysis for ImageJ/Fiji
Organization: mianalysis
fiji-plugin modular imagej image-processing image-analysis

montpellierressourcesimagerie / imagej_macros_and_scripts
imagej,ImageJ macros and scripts written at the imaging facility MRI
Organization: montpellierressourcesimagerie
imagej-macros imagej fiji-macro fiji bioimage-analysis image-analysis-workflows jython toolsets imagej-macro imagej-plugins

mrsutherland / xrm_reader
imagej,ImageJ plugin to read xrm files.
User: mrsutherland
imagej-plugins imagej fiji xradia zeiss xrm xrm-reader txrm txm

pmascalchi / imagej_auto-white-balance-correction
imagej,ImageJ / Fiji macro to automatically correct white balance in RGB images
User: pmascalchi
imagej macros fiji color-correction color-imaging color-camera colour-camera colour-correction whitebalance white-balance

pmascalchi / imagej_export-lif-as-individual-images
imagej,ImageJ / Fiji macro to automatically export Leica LIF file as individual images (batch mode available)
User: pmascalchi
lif export-lif macros imagej batch-mode fiji-macro imagej-macro leica confocal-microscopy

quantixed / cellmigration
imagej,Analysis of cell migration in Igor Pro
User: quantixed
cell-migration igor imagej tracking

quantixed / imagej-macros
imagej,quantixed FIJI update site + more
User: quantixed
imagej figure-maker tiff fiji fiji-macro imagej-macros

qupath / qupath
imagej,QuPath - Bioimage analysis & digital pathology
Organization: qupath
Home Page: https://qupath.github.io
bioimage-informatics image-processing digital-pathology pathology machine-learning cell-segmentation whole-slide-imaging bioimage-analysis cell-analysis imagej opencv groovy histology javafx tissue-microarray-analysis computational-pathology

rocsg / fijirelax
imagej,FijiRelax: 3D+t multi-echo spin-echo sequences MRI analysis
User: rocsg
Home Page: https://imagej.net/plugins/fijirelax
image-processing imagej imagej-plugins java modeling mri relaxation-time

ropensci / ijtiff
imagej,An R Package for general purpose TIFF file I/O which plays nice with ImageJ
Organization: ropensci
Home Page: https://docs.ropensci.org/ijtiff
r rstats tiff-files imagej tiff-images image-manipulation r-package peer-reviewed

scenerygraphics / sciview
imagej,sciview is a tool for visualization and interaction with ND image and mesh data
Organization: scenerygraphics
fiji imagej 3d visualization image-processing sciview scenery hacktoberfest

srmlabhust / qc-storm
imagej,Online processing plugin (Micro-Manager & ImageJ) for quality-controlled super-resolution localization imaging.
User: srmlabhust
Home Page: https://github.com/SRMLabHUST/QC-STORM
imagej localization-density localization-microscopy localization-precision micro-manager mle-localization

tferr / scripts
imagej,:microscope::cocktail: Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ
User: tferr
Home Page: https://imagej.net/BAR
image-analysis scripts-collection scientific-workflows microscopy imagej imagej2 java beanshell python jython

thorstenwagner / ij-blob
imagej,ImageJ library to detect and analyse connected components (blobs) in binary images
User: thorstenwagner
component-analysis image-analysis binary-image fiji imagej imagej-plugins

thorstenwagner / ij-nl-means
imagej,Non local means filter for ImageJ
User: thorstenwagner
denoising-images fiji imagej image-denoising

thorstenwagner / ij-ridgedetection
imagej,Detect ridges / lines with imagej
User: thorstenwagner
detect-ridges imagej fiji

uu-cellbiology / dom_utrecht
imagej,Detection of Molecules plugin for ImageJ, Utrecht University
Organization: uu-cellbiology
fiji-plugin imagej imagej-plugins java single-molecule utrecht-university

uu-cellbiology / zstackdepthcolorcode
imagej,Z-stack Depth Colorcode ImageJ FIJI plugin
Organization: uu-cellbiology
colorcode fiji fiji-plugin imagej imagej-plugin microscopy utrecht-university

wbif-bristol / imagej-fiji-level-1-course
imagej,Materials for the "ImageJ/Fiji Level 1: Basics of image processing and analysis" course taught at the Wolfson Bioimaging Facility, University of Bristol.
Organization: wbif-bristol
courses fiji image-analysis imagej

wbif-bristol / imagej-fiji-level-2-course
imagej,Materials for the "ImageJ/Fiji Level 2: Automation and batch processing using macros" course taught at the Wolfson Bioimaging Facility, University of Bristol.
Organization: wbif-bristol
batch-processing fiji-course imagej imagej-macro-language