Image Analysis resources

Introduction Talk

The slides of the intro talk can be found here

Useful Websites

• ImageSC Forum: great place for all image analysis related questions
• MIT DL Course: quick intro into deep learning
• Coursera: Andrew Ng offers several in depth courses on machine/deep learning
• iBiology: Introduction tutorials on imaging and image analysis
• Neubias: European Bio-image analysis network
• Intro to Bioimage analysis

Useful paper

• Great general intro to single cell analysis. BUT: the software list is already completely out of date and misses most modern deep learning based packages) Leygeber, 2019
• Great intro in reproducible workflows Miura, 2021

Useful papers for advanced feature extraction

This list mostly contains papers by ourselves, for the simple reason that we are familiar with the methods used in them. There are many other good papers out there from other labs too, of course!

• Accurately estimate cell length: Kiviet, 2014
• Estimate cell elongation rate: Dal Co, 2019
• Estimate lag time: Dal Co, 2019
• Estimate population growth rate using optical flow: Dal Co, 2019
• Estimate interaction range: Dal Co, 2020
• Correct fluorescent images: van Vliet, 2018
• Estimate promoter activity: Locke, 2011