Basic Introduction to 3D Biomedical Image Analysis with Fiji

19jan2:00 PM6:00 PMBasic Introduction to 3D Biomedical Image Analysis with Fiji

3D Biomedical

Event Details


Biological sciences often use imaging data from fluorescence microscopy to visualize biological processes in unprecedented detail.


However, assessment of the data often still relies on individual visual assessment rather than objective quantification. Thus, image analysis pipelines are required to allow data assessment in data in 3D+ to allow robust, scalable, and meaningful data analysis.

Methods: The open-source image analysis Fiji will be used to examine, enhance, segment, and quantify provided 3D data. After a one hour lecture, a 3-hour hands on tutorial will examine 3D+ data to provide hands-on practical examples to highlight image analysis workflows, and discuss image analysis in its wider implications.

Learning outcomes:


  • Understanding Data: 3D data understanding and analysis of optical fluorescence microscopy.
  • Image Analysis: Common image analysis steps such as data understanding, image enhancement, segmentation, and quantification.
  • Hands-on: Using hands-on exercises will provide the attendees with a broader understanding of quantitative image analysis.
  • Long-term: Using reflection after each step of the tutorial, attendees will be able to assess the importance and generalization of the learning material.



  • Participants are expected to follow along and participate.
  • Ideally participants know: what is Fiji, basic Fiji use, what are 3D data (i.e. how is an image basically constructed), etc.
  • Helpful tutorials:
  • Ideally, all attendees will participate in hands-on exercises and thus should bring/use their own laptops/computers. Data will be provided.



(Friday) 2:00 PM - 6:00 PM(GMT+00:00)

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