Resources
We are compiling a list of useful tools across different areas of microscopy: sample preparation, image acquisition, data analysis and image preparation. Please contact us using the contact form below or via scotmicro@outlook.com if you know of any other online resources that other microscopists would find useful.
General
Leica Science Lab
This Microscopy Knowledge Portal lets you learn, share and contribute microscopy knowledge. It offers scientific research and teaching material on micrsocpy-related topics, with the content designed to support beginners, experienced practitioners and scientists in their everyday work and experiments.
FocalPlane
FocalPlane is a microscopy community site, hosted by Journal of Cell Science and encompasses all fields where biology meets microscopy. This is a curated online meeting place to connect people, products, resources and information relating to microscopy.
Open Science
OMERO
OMERO is a client-server software for managing, visualising and analyzing microscopy images and associated metadata. As a scientist, OMERO can handle all your images using a secure central repository, from microscope to publication. Using the power of Bio-Formats, OMERO supports over 140 image file formats, including major microscope formats. The OMERO client is free to download.
Open Source Optics
Open source optics refers to optics, optical equipment, opto-electronics and fiber optic designs that are designed in the same fashion as free and open source software (FOSS). This is a collection of 3-D printable optical components.
https://www.thingiverse.com/jpearce/collections/open-source-optics
Lab On the Cheap
Information on lots of cheap, open source ways of populating everything you might need in biology and optics lab.
Image Analysis
Analysing Fluorescence Microscopy Images with ImageJ
This handbook aims to give you enough background to make it possible to progress quickly in bioimage analysis
https://petebankhead.gitbooks.io/imagej-intro/content/
IAFIG-RMS Python for Bioimage Analysis Course
This repository contains a Python Bioimage Analysis course which established the fundamentals of iamge analyusis in the context of biological imaging.
https://github.com/IAFIG-RMS/Python-for-Bioimage-Analysis
BioImage Analysis Series 2020
These lectures, run by Robert Hasse, will introduce you to many elements of bioimage analysis, from fiji useage and macro programming to use of ICY.
https://www.youtube.com/playlist?list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U
BioImage Analysis with Icy
This online webinar will walk you through the basics of doing image analysis with Icy
https://www.youtube.com/watch?v=5SJqhKjCbMQ&feature=youtu.be&app=desktop
Introduction to Bioimage Analysis
This lecture series covers bioimage analysis, from the basics up! https://www.youtube.com/channel/UC-hlwQ9Q4GS3rtv2EwSStAQ
Matlab
Learn how to use Matlab for free
https://matlabacademy.mathworks.com/
Microscopy Datasets
Nanotomy
These are large scale electron microscopy datasets that are freely available for researchers to use
Bioimage Archive
The BioImage Archive stores and distributes biological images that are useful to life-science researchers. Its development will provide data archiving services to the broader bioimaging database community.
Microscope Techniques
Lightsheet Microscopy Setups
Bruker provide webinars on different aspects of Lightsheet Microscopy:
Aurox: Microscopy and image analysis
Aurox have made a lot of their conference talks available, talking about a wide range of topics from different types of microscopy techniques to methods of image analysis.
https://www.youtube.com/channel/UCykKTH2IhFPRtQV0q31LP2w/videos
Data Analysis
An Introduction to R
This training course will introduce you to using R, an interactive environment for statistical computing.:
https://alexd106.github.io/intro2R/
Data Science for Ecologists and Environmental Scientists
This free resource is a selection of Coding Club tutorials, quizzes and practical challenges to increase your data manipulation, analysis and visualization skills
https://ourcodingclub.github.io/course