Faculty of Agriculture CSI Microscopy

Welcome to the Faculty of Agriculture CSI Microscopy GitHub organization! This repository serves as a resource hub for our users, providing essential tools, guides, and tutorials related to microscopy and image analysis.

Useful Links

• Instrument Booking Calendar
• Project Initiation Form
• Image Data Management
• Server Access Manual

Learning

Articles

• Understanding Numerical Aperture in Microscopy
• Resolution and Refractive Index
• Choosing a Fluorophore Palette
• Quantify Images in an Unbiased Way

Books

• BioImage Book: An introduction to bioimage analysis using open-source tools.

Tutorials

• Johanna M. Dela Cruz: Tutorials on optical microscopy, FIJI (ImageJ), and QuPath for multiplex fluorescence analysis.
• Robert Haase (haesleinhuepf): Fiji, CLIJ, Clesperanto, and more. From basics to Deep-Learning.
• MyScope Training: Comprehensive online training for various microscopy techniques.
• Light Field Microscopy Simulator: Interactive simulator to understand light field microscopy.
• Introduction to ImageJ: A comprehensive guide to getting started with ImageJ.
• Rescaling Images and Pixel Anisotropy: Insights on image rescaling and handling pixel anisotropy.
• Fiji Workshop Resources: Workshop resources for learning Fiji.
• Training materials for image analysis provided by the Weizmann Institute Cell Observatory.

Software

Image Analysis and Processing

• Fiji.sc
• Fiji Download
• Ilastik
• Icy
• QuPath
• QuPath Documentation
• Napari
• Napari Usage
• CLIJ
• clEsperanto
• pyclesperanto Prototype
• APEER
• Imaris
• Imaris Learning Resources
• Arivis
• Aivia

Startup/Shutdown Guides

• EVOS M7000 widefiled
• Stellaris STED Confocal
• Skyscan 1272 MicroCT
• SP8 Confocal - Work In Progress
• Luxendo MuVi SPIM Light Sheet - Work In Progress
• IT-100 SEM - Work In Progress
• JSM-7800 SEM - Work In Progress
• Liquid Nitrogen - Work In Progress

Data Handling Tools

• LIF to OME-TIFF Conversion Script
• Batch Processing with Fiji
• Automated Analysis Pipeline

Contributing

We welcome contributions from the community! If you have a tutorial, guide, or tool that you think would be beneficial, please follow our contribution guidelines.

Contact

For any questions or support, please reach out to us:

• CSI Email
• Einat Zelinger - Head of Unit
• Tally Kossovsky - Electron Microscopy and MicroCT
• Daniel Waiger - Light Microscopy, Image Analysis, 3D CAD modeling, and 3D printing