The Australian Microscopy & Microanalysis Society (AMMS) is a member-run society dedicated to the promotion of microscopy, microanalysis, and related techniques across a broad range of scientific disciplines. Our membership comprises professionals using microscopy techniques from universities, government labs, and industry, together with representatives of instrument manufacturers and their agents. AMMS incorporates several special interest groups including Volume Imaging Australia, Australian Microbeam Analysis Society, CryOz and Light Microscopy Australia.
Microscopy New Zealand brings together members of the microscopy community from throughout New Zealand.
The Microscopy Society of America is a non-profit organization dedicated to the promotion and advancement of techniques and applications of microscopy and microanalysis in all relevant scientific disciplines. They run major international conferences and have a range of focused interest groups.
The Royal Microscopy Society is an international microscopy society based in England, drawing members from all over the world. They run many meetings, conferences and workshops. They also have a range of focus groups including Image Analysis, Quality Control, Mass Spectrometry Imaging, X-ray Microscopy, and Ion Beam Microscopy.
Visit the International Federation of Societies for Microscopy for a full list of international microscopy societies.
The Volume EM community aims to support all those practically involved in volume electron microscopy techniques.
Global BioImaging is an international network of bioimaging facilities and communities. It brings together imaging facility operators and technical staff, scientists, managers and science policy officers from around the globe, to network, exchange experiences and build capacity internationally.
AI4Life: Horizon Europe-funded project that brings together the computational and life science communities, with the goal to develop tools and standards based on artificial intelligence (AI) methods for bioimage analysis (in particular microscopy image analysis)
foundingGIDE: Horizon Europe-funded project that aims to establish the basis of a coordinated Global Image Data Ecosystem that facilitates image data sharing and the exchange of bioimage data among major repositories, by developing common recommendations for ontologies and metadata, together with the wider global bioimage data community.
Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi): community initiative with members from academia and industry aiming at improving the reproducibility of light microscopy experiments in life and material sciences. QUAREP-LiMi publishes protocols and tools for Quality Assessment (QA) and Quality Control (QC) in light microscopy, tutorial videos, and automation scripts for microscopes. QUAREP-LiMi is working towards standardising vocabulary and formats to describe light microscopy instrumentation and experiments.
Australasian Electron Microscopy Email Group (AustEM) is an Australasian-wide email server set up by the Australian National University in 1995.
ImageJ Mailing List is a discussion group for ImageJ users and developers.
Confocal List Serve is an international mailing list dedicated to topics in confocal imaging.
3-Dimensional Electron Microscopy Mailing List is the primary communication source among experts in the field of molecular and cellular electron microscopy. Postings include upcoming conferences, announcements, job listings and technical queries.
Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM) supports users and developers in biological electron microscopy. CCP-EM aims build a community for computational aspects of cryo-EM.
IMOD Discussion Group and Mailing List is a mailing list and forum for imod software used to process tomography data. It provides a forum for users to pose questions or present problems, offer solutions to others’ problems, or make suggestions about improvements. The mailing list is used to send notices of new versions or other general news.
The SerialEM Discussion Group provides a means for users and people managing the program to ask questions and share their experiences, as well as a way to receive notification of new releases and other news. SerialEM is a program that can acquire a variety of data from electron microscopes with a focus on automated tilt series acquisition for electron tomography.
Royal Microscopy Society Image Analysis Resources
Fiji is an image processing package—a “batteries-included” distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. Cameron Nowell from Monash University has developed an extensive Fiji Training Manual that he makes openly available.
Python is a high-level, general-purpose programming language. There are some great free resources for image processing using Python such as Image Processing with Python, Medical Imaging Processing with Python, Beginner Python Image Analysis Course or Introduction to Deep Learning with Python
Imaris Viewer is a free 3D/4D microscopy image viewer for viewing raw images as well as those analysed within Imaris.
PhotoPea is a free, online alternative to Photoshop. It can be used to adjust and colour micrographs. For information, watch our beginners guide to colouring micrographs on YouTube.
Web-based virtual desktops for data analysis or processing that use advanced computing infrastructures such supercomputers or clouds. Some Australian options include:
Electron Microscopy Data Processing Portal: access to CryoSPARC and LiberTEM
Australian Research Environment: requires an NCI account. If you do not have one, you can sign up here.
Globus: Service developed for researchers and research organisations that provides fast, reliable, secure and high-assurance data transfer
FileSender: Web-based application developed by AARNet for sending files anywhere in a secure way (end-to-end encryption) without the need for the recipient to have an account
The Electron Microscopy Data Bank (EMDB): free, public repository for cryo-EM volumes and representative tomograms of macromolecular complexes and subcellular structures.
Electron Microscopy Public Image Archive (EMPIAR): free, public repository for raw images underpinning 3D cryo-EM maps and tomograms (themselves available in EMDB). 3D datasets from volume EM techniques and soft and hard X-ray tomography can also be uploaded to EMPIAR.
World Wide Protein Data Bank (wwPDB): free, public repository of 3D structures of proteins, nucleic acids, and complex assemblies. Data are stored in all current members of wwPDB, namely: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, USA, https://www.rcsb.org/), Protein Data Bank in Europe (PDBe, https://www.ebi.ac.uk/pdbe/), and Protein Data Bank Japan (PDBj, https://pdbj.org/), Biological Magnetic Resonance Bank (BMRB, https://bmrb.io/) and Electron Microscopy Data Bank (EMDB, https://www.ebi.ac.uk/emdb/). The member sites are more than just mirrors as they offer different tools on their websites for analysing the structures in the database. PDB stores any atomic models that have been constructed based on EMDB data.
BioImage Archive (BIA): Free, publicly repository of biological images from any imaging modality, as long as the data are either associated with a peer-reviewed publication, or of value beyond a single experiment.
Image Data Resource (IDR): public repository of high-quality bioimage datasets from published scientific studies
Prometheus Wiki: Protocols in ecological & environmental plant physiology
