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Techniques
Image Analysis
Image Analysis Forum: image.sc
An image analysis discussion forum
Quantitative Imaging: From Acquisition to Analysis
14 days
in Cold Spring Harbor, NY
Future dates TBA
BIG DATA I: Visualization, File Formats & Processing in Fiji, virtual
Begins 2021-01-14
This event will take place online
BioImage analysis with Fiji/ImageJ
in Charleston, SC
Online Course
Advanced methods in biomedical image analysis
1 days
Online Course
Course starts on 2020-10-02
Introduction to Light and Fluorescence Microscopy
Free online theory lectures
Mesmerize: A highly versatile platform for calcium imaging analysis
Platform for Calcium imaging analysis
Created by Kushal Kolar, Daniel Dondorp, Marios Chatzigeorgiou
Open source
SPIMagine
GPU accelerated volume rendering
Created by Weigert M
Open source
Mastodon
Tracking and track-editing framework
Open source
Advanced Cell Classifier
Machine learning method for image data analysis
Created by Horvath Lab
Open source
Nucleaizer.org
A cell segmentation tool
Created by Horvath Lab
Open source
CIDRE
A flatfield illumination correction method
Created by Horvath Lab
Open source
Napari
Fast ND image viewer for python
Created by Sofroniew, Royer, Nunez-Iglesias et al (doi:10.5281/zenodo.3555620)
Open source
CSBDeep
A toolbox for Content-aware Image Restoration (CARE)
Created by Weigert M et al
Open source
Bioimage Data Analysis Workflows
Open Access textbook on image analysis
AIDAhisto
A tool optimised for quantification of histological staining of mouse brain tissue
Created by Niklas Pallast and Markus Aswendt
Open source
Python for Microscopist Videos
YouTube channel with educational videos on Python coding
Bioimage Analysis Course: Life cycle of an image data set
Online Course
Image Tools Resource
List of open-source analysis software for bioimaging
Created by Image Data Resource
Open source
FrapCalc
Analyzes FRAP curves with various models
Created by K Miura
Open source
easyFRAP
Quantitative and qualitative analysis of FRAP data
Created by Lygerou Lab
Open source
EAMNET Downloads
Links to Macros and software packages
Created by EAMNET
Open source
BioImage Data Analysis
An open access text book on 'BioImage Data Analysis'
PyImageSearch
Object-recognition with Python/OpenCV
Multi-view simulation
Code for simulating a multiview acquisition
Created by Preibisch Lab
Open source
Multi-view reconstruction
Software for reconstruction of multiview images
Created by Preibisch Lab
Open source
BigStitcher
Stitching for large datasets
Created by Preibisch Lab
Open source
BioImage Archive
A hub for biological images
Created by EMBI-EBI
Open source
Deep Learning for Image Analysis
5 days
in Heidelberg, Germany
Online Course
Applications due on 2020-11-16
Course starts on 2021-02-08
TOOL-AI
A blog about tools for image analysis
QuPath
software for whole slide image analysis
Created by Pete Bankhead and Jose Fernandez
Open source
Bioimage Data Analysis
Software overview and examples of image analysis
pyCUDAdecon
Python wrapper for cudaDecon - 3D deconvolution
Created by Talley Lambert, Harvard Medical School
Open source
Danuser Lab Software
Several different software packages available
Created by Danuser Lab, UTSW
Open source
Image Data Resource
Online, public data repository
Created by University of Dundee & Open Microscopy Environment
Open source
Analyzing Fluorescence Microscopy Images with ImageJ
An online ImageJ textbook
Image Analysis with Fiji
Online Course
Pixel Chart
Created by Andrei Kashcha
Open source
PatternUnmixer 2.0
Object type recognition for automated analysis
Created by Murphy Lab, Carnegie Mellon
Open source
CellOrganizer
Model learning tools
Created by Murphy Lab, Carnegie Mellon
Open source
ilastik
Interactive learning and segmentation toolkit
Created by Anna Kreshuk's lab, EMBL
Open source
BioImageXD
Analyzing, processing & visualizing nD images
Open source
BisQue
Store, visualize, organize and analyze in the cloud
Created by UCSB Center for Bio-image Informatics
Open source
Image Analysis Focused Interest Group
Content to support the image analysis community
Created by Royal Microscopy Society
Open source
PSFj
Software for point spread function analysis
Created by Knop Lab, ZMBH
Open source
FIJI
ImageJ bundled with a lot of plugins
Created by Curtis Rueden & the ImageJ development team at LOCI, U. Wisconsin-Madison
Open source
CellProfiler
For measuring and analyzing cell images
Created by Carpenter Lab, Broad Institute
Open source
Image and Data Analysis Core Software List
A list of open-source software for image analysis
Open source
Icy
Platform for bioimage informatics
Created by Quantitative Image Analysis Unit, Institut Pasteur
Open source
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