Light Microscopy : Resources

Our resources

Slides

• Introduction to light microscopy – part 1 (basics)
• Introduction to light microscopy – part 2 (fluorescence) 
• Introduction to live cell imaging
• Introduction to multiphoton microscopy
• Introduction to optical sectioning
• Introduction to confocal laser scanning microscopy
• Introduction to light-sheet microscopy
• Introduction to image analysis with FIJI
• Introduction to OMERO@Crick (Jun 2022)
• Introduction to sample prep and basic fluorescence imaging (2024)

Videos

• Introduction to light microscopy – Kurt Anderson (2023)

Basic digital imaging

• Book chapter in 'Basic Digital Image Acquisition, Design, Processing, Analysis, Management, and Presentation'
• Image analysis protocols (GitHub)

GitHub repositories

• https://github.com/FrancisCrickInstitute/CALM
• https://github.com/djpbarry/Giani
• https://github.com/RoccoDAnt/napari-zelda
• https://github.com/RoccoDAnt/napari-superres

More OMERO content by Kenneth Ho

• Crick’s OMERO Guide (Nov 2023)
• Introduction to OMERO@Crick (Jun 2022)
• Manage your image data and workflow (Mar 2023)
• Manage your digital image data (Dec 2021)

Image data science with python and napari

Additional resources

This Jupyter book contains training resources for scientists who want to dive into image processing with Python and Napari.

Created by the LIBRE hub project (Latin American Hub for Bioimaging Through Open Hardware).

Defragmentation Training School – NEUBIAS Academy & EOSC-Life 2022

A training school for the new generation of bioimage analysts. Topics: workflow-based image analysis and new integrated methods for cloud computing applied to life sciences.

Scientific Organizers: Rocco D'Antuono, Paula Sampaio, Mafalda Sousa, Clara Prats, Marion Loveaux.

IAFIG-RMS/Python-for-Bioimage-Analysis 2

This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging. - IAFIG-RMS/Python-for-Bioimage-Analysis

Dominic Waithe, Chas Nelson, Dominic Waithe, Mikolaj Kundegorski, Stephen Cross and Todd Fallesen.

Here is a selected list of websites providing online training:

• Olympus Microscopy Resource Center: definitions, descriptions, and articles covering basic and advanced concepts in light microscopy.
• Zeiss Education in Microscopy and Digital Imaging: definitions, descriptions, and articles covering basic and advanced concepts in light microscopy.
• iBiology Microscopy Series: microscopy concepts and methods explained in 30-minute talks.
• Recorded Talks & Lectures: A large and slightly random collection of links to high-quality online microscopy resources hosted by the Royal Microscopy Society (click on the ‘Recorded Talks & Lectures’ tab near the top of the page).
• Tutorial on the use of Zeiss LSM880: Imaging facility del Baylor College of Medicine