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September 2019

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October 2020

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. 

https://www.leica-microsystems.com/science-lab/

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.  

https://focalplane.biologists.com/

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.

https://www.openmicroscopy.org/

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.

https://www.labonthecheap.com/

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

http://www.nanotomy.org/ 

 

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.

https://www.ebi.ac.uk/bioimage-archive/

Microscope Techniques

Lightsheet Microscopy Setups

Bruker provide webinars on different aspects of Lightsheet Microscopy:

https://www.bruker.com/nc/products/fluorescence-microscopes/luxendo-light-sheet-microscopy/resources.html

 

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