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External resources

  • This is a curated, non exhaustive, list of useful links pointing at training courses, knowledge bases, and tutorials. The topics or software addressed here are intended to cover what is currently available at the platform.
  • The CIF has no relationship with any of the commercial links presented here, and this list is only meant to help the researcher in his daily work.
  • The links are presented in no particular order, but they are sorted by category.
  • If you see any broken link, please tell us immediately using the contact form on the bottom of the home page to keep this page as relevant as possible. You can also submit new links or ideas the same way.

Data Management

How to organize your data

This is probably the most important thing you have to master before focusing on any other imaging problems.

Topic Description Link Type

UNIL Open Science Data

Data management plan, file naming, folder structure

Best practices for scientific computing

[…]This paper describes a set of practices that are easy to adopt and have proven effective in many research settings. Our recommendations are based on several decades of collective experience both building scientific software and teaching computing to scientists [17],[18], reports from many other groups [19]–, guidelines for commercial and open source software development [26],, and on empirical studies of scientific computing [28][31] and software development in general (summarized in [32]). […]

Good enough practices in scientific computing

[…]This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. […]

Image Processing

ImageJ | FIJI

Image J is the go-to open-source image processing software for many scientists. The FIJI distribution is a complete package dedicated to the biologist and microscopist

Topic Description Link Type

ImageJ Techniques

General ImageJ concepts, skills, and techniques
FIJI Scripting Tutorial Learn how to program FIJI scripts in Python
ImageJ user guides E-Books and recommended books
FIJI for Cell segmentation
Video tutorial by the Melbourne Advanced Microscopy Facility Youtube video


Imaris is a commercial package focusing on 3D data sets, whether they are stacks, multichannel, time series, or any other data requiring 3D visualization and processing.

Topic Description Link Type

Bitplane learning center

Collection of video tutorials, webinars recordings and white papers from Bitplane


Image processing software package that focuses on data sets coming from slide scanners, but can be applied to other types of images as well.

Topic Description Link Type

Getting started

Video walkthrough by QuPath’s author, Pete Bankhead

Youtube playlist

Case study : IHC analysis

Advanced topics with QuPath

Youtube playlist


Image processing software package that focuses on large data sets composed of possibly millions of files. Idealy suited for high throughput content, but it can also be used on single images as well. The learning curve is quite steep.

Topic Description Link Type

CellProfiler Overview

Video walkthrough by Gopal Karemore (workshop recording)

Youtube video

Borad Institute tutorials

Various use cases by the group behind Cell Profiler at the Broad Institute. From beginners to cell classification via machine learning.

Youtube playlist

General Imaging

Fluorescence staining

Most of modern optical optical microscopy is based on fluorescent probes. You will find here links related to their use in microscopy.

Topic Description Link Type

Handbook of Fluorescent Probes

The complete Molecular Probes book on fluorescent dyes. Probes for each and every use case

Primers and Knowledge Bases

Knowledge bases are covering all the key microscopy concepts. They are often written by microscopy companies to help their customers, but they also address more general topics, independently from their products. You will also find extensive documentation on brand-specific technologies like Zeiss Airyscan or Leica STED.

Topic Description Link Type

Olympus Microscopy Resource Center

Covers topics ranging from the physics of light to virtual microscopy.

Nikon Microscopy U

Website dedicated to microscopy education. Many articles on key concepts of all imaging domains, from physics, to detectors and cameras, and even ideal posture in front of a microscope
Zeiss Campus Same principle as other similar knowledge base, with interactive tutorials and techniques review articles
Leica Science Lab
Also similar to the other education sites by microscopy brands, there a re interactive tutorials, webinars recordings, as well as a community aspect to it.