The course has a very strong focus on fluorescent micrographs! There will be NO analysis of gels or Western blots. Images from immunohistochemical stainings (non-fluorescent) will also be partially discussed, since processing is in parts similar. 

The difficulty level is medium and easy to follow in step by step procedures and in-depth explanation of the necessary background to the individual methods. Also scientists with some prior knowledge will still benefit from the methods taught.

Content

• Overview over proper scientific image file formats, metadata, bit depth
• In-depth practical introduction to pre-processing
  • Automatic uneven lighting correction
  • Understanding of image filters and their use cases for improved object detection
  • Automatic background subtraction algorithms to reduce unspecific signal
• Object segmentation with automatic intensity thresholds (semantic segmentation)
• Individual object labeling (instance segmentation)
• Basic insight into some user friendly machine learning plugins in comparison to classical segmentation
• Optimization of segmentation with post-processing methods
• Quality control of segmentation results
• Different basic automatic analyses (object counting, measurements, shapes, intensities)
• Optional dependent on time: How to deal with 3D data in image analysis
• Short introduction to macro recording for automation.

Aim

In the workshop, participants will learn how to efficiently process and analyze microscopic images. They will gain in-depth insights into the methods and techniques necessary to extract precise information from their microscopic images. The focus will be on practical application and on the "Do's" and "Don'ts" of image processing to achieve valid and scientifically accurate results.

Target Group

Doctoral Researchers and Postdocs from the first year of the PhD phase and beyond. Participants should ideally have some practical experience in image processing. The course is especially suitable for those who have already attended the first BioVoxxel workshop "Scientific Image Editing and Figure Creation" and have basic knowledge in handling scientific images, metadata, and the image histogram.

Method

The workshop combines interactive live lectures with practical exercises in a virtual format. During the course, we will exclusively use a customized version of Fiji (ImageJ bundle). Fiji is free, open-source, and easily accessible. Prior knowledge of the software is not required, but it may be helpful.

All registered participants will receive detailed instructions for preparation and software installation via email in advance of the workshop.

Pre-requisites:

This workshop builds up on some basic knowledge from Scientific Image Editing and Figure Creation but can be done independently

Best 2 monitors to watch the workinar on one and do the practical part on the other.

Possibility to install software on your computer (or administrator rights).