LMA-SA FIJI and Friends- AI and ML Advanced Workshop 2024

The Fiji distribution of the ImageJ image analysis package is a powerful free tool. This workshop will explore Artificial Intelligence and Machine learning using FIJI and other freeware including Ilastik, StarDist, and more.

Artficial Intelligence (AI) and Machine Learning (ML) guided image analysis can greatly accelerate existing workflows or allow extraction of data from images that is just not possible any other way. The AI landscape is constantly evolving and changing. The upside of this is that there is potentially something new to address current shortfalls, something that was impossible a couple of months ago may now be routine. This flexibility and adaptability comes at a cost however. Getting the right environment and analysis pipeline working can be a challenge. Additionally functional pipelines can suddenly fall over due to updates or other incompatibilities that creep in. These issues (setup, running and maintaining) can be worked around through the vast amount of resources available on the internet. Unfortunately, a lot of these resources are aimed at computer science professionals and not your average scientist trying to do some image analysis. This workshop including notes and examples will help to demystify as much of this process as possible by providing a series of environments that will work to carry out all or parts of the following -Nuclei and other round object segmentation using StarDist -Including training and using custom models -Cell segmentation using CellPose -Including training and using custom models -Segmentation and selection of specific image areas (intensity, colour, texture) using Ilastik -Denoising using Noise 2 Void in Napari -Incorporating outputs from these various systems into Fiji macro code to allow automated analysis of many images. The notes provided are for using the CPU for any computation. GPU computation greatly improves the speed of model learning and running but setting up the software is very hardware version specific. For ease of use and setup the notes provided will only use the CPU.

LMA Members: $90 (join AMMS/LMA at https://microscopy.org.au)

General: $120

Students: $120

Retired Scientists: $120

Cost includes

• ·Colour print-out of NEW manual!
• ·USB with manual and demo images
• ·Morning and afternoon tea