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Techniques
Image Analysis
Image Analysis Forum: image.sc
The image analysis discussion forum
Quantitative Imaging: From Acquisition to Analysis
Format: In-person
Location: Cold Spring Harbor, NY
Starts on 2022-03-29
Microscopic Image Analyzer (MIA)
A software for deep learning based image analysis
Created by Nils Körber
Bioimage Model Zoo
Advanced AI models in one-click
Open Source 3D Printed Microscope
PUMA 3D Printed Microscope
Created by Dr Paul J. Tadrous
Licensed by GPL v3.0
Introduction to Modern Statistics
Free online textbook
Center for Open Bioimage Analysis YouTube Channel
CellProfiler tutorials
Python tutorials for image processing
Python tutorials for image processing
Quantitative Phase Microscopy Software interface
GPU DHM
Created by Lee Lab @JCSMR
Deep Learning Based Segmentation For Biologists
An online workshop
Bioimage Informatics Index
An extensive database of image analysis tools
Created by NEUBIAS
Image Analysis Methods for Biologists
A 4-week online course
Python Bioimage Computing Toolkit
Python functions, scripts, and classes
Created by Marcelo Cicconet
Image to Knowledge (I2K) Tutorials
Image analysis tutorials from I2K
Image Processing and Analysis for Life Scientists
A self-paced ~7 week online course
BioImage Analysis Workshop
5 session workshop on bioimage analysis
FIJI Image Processing and Analysis Workshop
PDF slides and reference list
BioImage analysis with Fiji/ImageJ
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
SPIMagine
GPU accelerated volume rendering
Created by Weigert M
Mastodon
Tracking and track-editing framework
Advanced Cell Classifier
Machine learning method for image data analysis
Created by Horvath Lab
Nucleaizer.org
A cell segmentation tool
Created by Horvath Lab
CIDRE
A flatfield illumination correction method
Created by Horvath Lab
Napari
Fast ND image viewer for python
Created by Sofroniew, Royer, Nunez-Iglesias et al (doi:10.5281/zenodo.3555620)
CSBDeep
A toolbox for Content-aware Image Restoration (CARE)
Created by Weigert M et al
AIDAhisto
A tool optimised for quantification of histological staining of mouse brain tissue
Created by Niklas Pallast and Markus Aswendt
Python for Microscopist Videos
YouTube channel with educational videos on Python coding
Bioimage Analysis Course: Life cycle of an image data set
Graduate student level introduction to bioimage analysis
Image Tools Resource
List of open-source analysis software for bioimaging
Created by Image Data Resource
FrapCalc
Analyzes FRAP curves with various models
Created by K Miura
easyFRAP
Quantitative and qualitative analysis of FRAP data
Created by Lygerou Lab
EAMNET Downloads
Links to Macros and software packages
Created by EAMNET
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
Multi-view reconstruction
Software for reconstruction of multiview images
Created by Preibisch Lab
BigStitcher
Stitching for large datasets
Created by Preibisch Lab
BioImage Archive
A hub for biological images
Created by EMBI-EBI
TOOL-AI
A blog about tools for image analysis
QuPath
software for whole slide image analysis
Created by Pete Bankhead and Jose Fernandez
Image to Knowledge (I2K): ImageJ User and Developer Conference
Starts on 2022-05-09
Location: Madison, WI, USA
pyCUDAdecon
Python wrapper for cudaDecon - 3D deconvolution
Created by Talley Lambert, Harvard Medical School
Danuser Lab Software
Several different software packages available
Created by Danuser Lab, UTSW
Image Data Resource
Online, public data repository
Created by University of Dundee & Open Microscopy Environment
Analyzing Fluorescence Microscopy Images with ImageJ
An online ImageJ textbook
Image Analysis with Fiji
Slides & test data
Pixel Chart
Learn how an image histogram is formed
Created by Andrei Kashcha
PatternUnmixer 2.0
Object type recognition for automated analysis
Created by Murphy Lab, Carnegie Mellon
CellOrganizer
Model learning tools
Created by Murphy Lab, Carnegie Mellon
ilastik
Interactive learning and segmentation toolkit
Created by Anna Kreshuk's lab, EMBL
BioImageXD
Analyzing, processing & visualizing nD images
BisQue
Store, visualize, organize and analyze in the cloud
Created by UCSB Center for Bio-image Informatics
Image Analysis Focused Interest Group
Content to support the image analysis community
Created by Royal Microscopy Society
PSFj
Software for point spread function analysis
Created by Knop Lab, ZMBH
FIJI
ImageJ bundled with a lot of plugins
Created by Curtis Rueden & the ImageJ development team at LOCI, U. Wisconsin-Madison
CellProfiler
For measuring and analyzing cell images
Created by Carpenter Lab, Broad Institute
Image and Data Analysis Core Software List
A list of open-source software for image analysis
Icy
Platform for bioimage informatics
Created by Quantitative Image Analysis Unit, Institut Pasteur
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