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
  • Understanding of image filters and their use cases for improved object detection
    
  • Diverse automatic algorithms to reduce unspecific signal
• Classical object segmentation (semantic), including quality control considerations
• Individual object labeling (instance segmentation)
• Insight into machine learning-based segmentation and comparison to classical methods
• Optimization of segmentation with post-processing methods
• Quality control of segmentation results
• Different basic automatic analyses (object counting, measurements, shapes, intensities)
• Short introduction to macro recording and batch processing for automation
• Diverse image segmentation examples as orientation for optimizing image analysis pipelines

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

Category:

GSP / Data Analysis / Hard Skills

Venue:

The workshop will be held as a virtual live workinar with many hands-on sessions via Zoom.

Course Language:

• English (trainer can also communicate in Spanish)
  

Duration:

2 days, each plan some buffer time

Time Zone Info:

• Mexico City: 07:00 AM - 01:00 PM
• Bogota / Houston: 08:00 AM - 02:00 PM
• Santiago / Boston: 09:00 AM - 03:00 PM
• Buenos Aires / Rio d.J.: 10:00 AM - 16:00 PM
  

Price:  

• EUR 149.00 special price for Latin American Academia  (early bird EUR 129.00, first 5 tickets) eligible only for people located in Latin America
• EUR 199.00 Europe / US / Industry  (early bird EUR 179.00, first 5 tickets)

Certificate:

Participants receive an official certificate of participation, listing the workshop content after actively attending minimally 85% of the 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 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.

Difficulty Level:

The difficulty level is intermediate 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.

Pre-requisites:

• This workshop assumes some basics from Scientific Image Editing and Figure Creation but can be done independently
• 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)

Software:

During the course we will exclusively work with a customized version of Fiji (ImageJ bundle) Fiji is free of charge, accessible for everybody and open source. Prior software knowledge is not required but might be of advantage.

Registered participants will receive all information regarding software preparation on time before the workshop via email.