Incorporating Machine Learning Tools into Image Analysis Workflows using Fiji, Ilastik and Stardist

Overview

This repository include Material used during hands-on tutorial workshop given at the Israeli Society of Microscopy 2023 meeting: Presentation, Exercises and related image files.

A typical image analysis workflow includes segmentation of regions and objects (eg nuclei or cells), measuring multiple features for objects and regions, and quantifying relations between objects. Fiji is an open-source software platform based on ImageJ and a collection of compatible plugins focusing on general purpose image analysis for life-sciences. It is scriptable and enables fast prototyping of image analysis workflows. Ilastik, StarDist and other Fiji plugins provide an easy way to exploits recent advances in machine-learning and deep-learning based algorithms as handy components for use within image analysis workflows. In this hands-on workshop we introduce building image analysis workflows using Fiji, Ilastik and StarDist.

This workshop does not cover the basics of image analysis. If you are not familiar with this, we highly recommend you to go through one of the following resources: Mooc on Image Processing and Analysis for Life Scientists by EPFL image analysis team, OR Introduction to Bioimage Analysis by Pete Bankhead. Please make sure to follow the Get Prepared section in order to install the software used at the workshop.

Workshop outline:

1. Nuclei segmentation using StarDist
2. Learn Ilastik, train Pixel classifier for Osteoclasts (OCL)
3. Use Ilastik from Fiji
4. Pixel > Objects
5. Parent Child relation: BioVoxxel Object Inspector plugin
6. Measurements & QualityControl
7. Automation guidelines I: Recordings > Single file macro
8. Automation guidelines II: Processing whole folder
9. Use Fiji macro to process a whole folder

To follow the exercise use the presentation (ISM2023-Workshop-Fiji-Ilastik-StarDist.pdf) and related detailed instructions (Fiji_Ilastik_StarDist_Workshop_ISM-2023.pdf)

For further Ilastik training - which was shown interactivly during the workshop - we recommend watching Ilastik I2K-2022 tutorial or Ilastik NEUBIAS webinar. For further StarDist training: see Stardist NEUBIAS webinar. For further Fiji macro writing: see NEUBIAS Fiji Macro webinar

Data used within this tutorial is courtsey of Dr. Sabina Winograd-Katz and Prof. Benny Geiger, Weizmann Institute of Science