Basic Microscopic Image Processing and Analysis - VIRTUAL WORKSHOP

Main Target Group and Focus:

• Life or Natural Scientists starting PhD-student level (1st year) and above.
• Optimally, some practical imaging experience is an advantage.
• Optimally, you have visited the first BioVoxxel Workshop Scientific Image Editing and Figure Creation and/or have some prior knowledge on proper scientific image handling, metadata, the image histogram, …

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.

Detailed workinar content overview:

• Short Introduction to Fiji / ImageJ and basic functions
• Overview over proper scientific image file formats, metadata, bit depth
• In-depth practical introduction to pre-processing
  • Automatic uneven lighting correction
  • Image filters for improved object detection and noise removal
  • 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.

All methods are learned hands-on with plenty of practical exercises to get confidence in applying them in your daily work.

Pre-requisites:

• This workshop builds up on some basic knowledge from Scientific Image Editing and Figure Creation
• Computer or Laptop (PC or Mac; supported operating systems: Windows, MacOS and Linux)
• Stable internet connection
• Mouse and Headset/Microphone
• Optimally a webcam
• Best 2 monitors to watch the workinar on one and do the practical part on the other.
• Proficiency in handling your computer in general
• Possibility to install software on your computer (or administrator rights)

To attend, please register here.

Note: Registration of GSLS/GSST doctoral researchers has priority to non-GSLS/non-GSST participants. Non-GSLS/non-GSST participants pay a service and workshop fee of EUR 50 by bank transfer.