Resources for learning more#

Resource Name


Brief description

🌐 39


Discussion forum for bioimage analysis software

🌐 Peter Bankhead’s Intro to Bioimage Analysis


Guide for absolute beginners to image analysis, including embedded questions/answers, exercises with Python and ImageJ, and videos to check understanding

📖 Bioimage Data Analysis 40


A free online textbook introducing various topics by Bioimage Analysis experts, edited by Kota Miura

📄 Reproducible image handling and analysis 41


An article reviewing major pitfalls in image handling and how to avoid them and create reproducible analysis workflows

📄 Made to measure: an introduction to quantification in microscopy data

link 42

An article describing several common classes of measurements made in microscopy data, as well as technical factors that may affect the results

🌐 Metrics Reloaded


An interactive guide to choosing the right metric for your scientific question

📄 A Hitchhiker’s guide through the bio-image analysis software universe 3


An article that gives guidance and a glossary of available image analysis software and packages

🌐 BioImage Informatics Index


Repository platform for searching bioimage analysis tools and workflows based on the problem, method or software of choice

🎥 iBiology Bioimage Analysis video series


Video series that introduces Bioimage analysis, including overviews of image processing, segmentation, tracking, making and interpreting measurements, tips and pitfalls

🌐 Bioimage ANalysis Desktop (BAND)


Access to virtual desktops allowing access to bioimage analysis software from a browser

🌐 Galaxy Imaging Node


A Galaxy node prepopulated with a number of open-source image analysis tools and workflows, making it easy to create and share reproducible FAIR workflows

🌐 Image Analysis Training Resources


Image analysis traning resources collected by NEUBIAS, styled based on The Carpentries

🌐 Bioimage Analysis AwesomeList


A curated AwesomeList of resources related to bioimage analysis

🌐 Bioimage Analysis Notebooks


A collection of Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more