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.
- Project Initiation Form
- Image Data Management and Remote Access
- Image Analysis Server Access Manual - For HUJI Users
- Understanding Numerical Aperture in Microscopy: Explanation of numerical aperture and its significance in microscopy.
- Resolution and Refractive Index: Setting Up Your Confocal Microscope: Guidance on how to set up your confocal microscope considering resolution and refractive index.
- Choosing a Fluorophore Palette: Tips for selecting the right fluorophores for your experiments.
- Quantify Images in an Unbiased Way: Techniques for unbiased image quantification.
- BioImage Book: An introduction to bioimage analysis using open-source tools.
- Johanna M. Dela Cruz: Listen, watch and learn optical microscopy and image processing & analysis with FIJI (ImageJ), and a tutorial series on multiplex or multispectral fluorescence analysis of whole slide images with QuPath.
- 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.
- Image Analysis Training Material: Training materials for image analysis provided by the Weizmann Institute Cell Observatory.
- Fiji: An open-source platform for biological-image analysis.
- Fiji Software: Download and documentation for Fiji, an image processing package.
- Ilastik: User-friendly tool for image classification and segmentation.
- Icy: An open-source software for bioimage analysis.
- QuPath: Open source software for digital pathology and bioimage analysis.
- QuPath Documentation: Comprehensive documentation for using QuPath.
- Napari: Multi-dimensional image viewer for Python.
- Napari Usage: Detailed guide on how to use Napari.
- CLIJ: GPU-accelerated image processing in ImageJ/Fiji.
- clEsperanto: Open-source platform for GPU-accelerated image processing.
- pyclesperanto Prototype: Python library for GPU-accelerated image processing.
- APEER: A platform for microscopy image analysis and sharing. It is a web-based annotation tool for machine- and deep-learning that allows users to create training datasets by painting pixels and annotating multidimensional datasets, coding-free.
- Imaris: Software for 3D and 4D microscopy image visualization and analysis.
- Imaris Learning Resources: Tutorials and resources for learning Imaris.
- Arivis: Solutions for 3D and 4D image visualization and analysis.
- Aivia: Advanced image analysis software for scientific imaging.
- Nyquist Calculator: A tool for calculating the Nyquist sampling rate for microscopy.
- Image.sc Forum: A community forum for discussion and image analysis questions.
Quick reference guides to help you efficiently start up and shut down your microscopy equipment:
- 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
- IT-100 SEM - Work In Progress
- Liquid Nitrogen - Work In Progress
Explore our collection of scripts and tools for handling data from various microscopes:
- LIF to OME-TIFF Conversion Script: Script for converting LIF files to OME-TIFF format.
- Batch Processing with Fiji: Guide for batch processing images using Fiji.
- Automated Analysis Pipeline: Pipeline for automated analysis of microscopy data.
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.
For any questions or support, please reach out to us: