Resources
Here are some useful tools and references developed by our members:
Software & Tools
- napari
a Python library for n-dimensional image visualisation, annotation, and analysis. Website - Cecelia
a multifunctional image analysis toolbox for decoding spatial cellular interactions and behaviour. github - napari-lattice
a python package for deskewing, cropping, visualisation (with napari plugin), and analysis of lattice light sheet data. github
Tutorials & Learning
- Fiji Training Notes Google Site
Cameron Nowell’s famous and comprehensive FIJI manual. - BOMP Workshops and Resources BOMP
Videos, PDFs, and links to workshops from the University of Melbourne The Biological Optical Microscopy Platform (BOMP). - IMB Microscopy Playlist IMB Youtube
Youtube channel of the microscopy facility at University of Queensland’s Institute for Molecular Bioscience.
Publications & Guidelines
-
Cecelia: a multifunctional image analysis toolbox for decoding spatial cellular interactions and behaviour Nature Communications
-
Big Brains, Small Targets: Whole-Brain Image Analysis with Python YouTube Link
Ishrat Zaman’s presentation at PyCon AU 2025.
Other Resources
Presented here is a list of links to things that have come up in our monthly meetings
September Meeting
- ZIDAS 2025 Switzerland’s Image & Data Analysis School
Website - EPFLx: Image Processing and Analysis for Life Scientists
A self guided, online image anlaysis curriculum from EPFL. Website - CoLoc
A collaborative board game to teach co-localization analysis. github - Certificate in Small-Group Teaching (CSGT)
Something to consider for new trainers - currently only open to Unimelb staff and graduates. webite
October Meeting
- Nextflow
Pipeline manager for “simpler” HPC processing and parallelisation Website - SODA-Hub
Spatial Omics Data Analytics Hub at WEHI Website - SOPA Github Repo
Spatial Omics Pipeline and Analysis github - TabPFN
Foundation model for Tabular Data github
If you have a resource to share, let us know!