The CORBEL webinar series continues with a basic introduction to bioimage analysis by Christian Tischer, from the EMBL Centre for Bioimage Analysis (CBA). During this webinar, Christian Tischer will explain basic concepts of (automated) bioimage analysis. The webinar includes a short overview of what bioimage analysis actually is and why it is useful. Subsequently, image formation, restoration, filtering and segmentation will be addressed, as well as object measurements and image analysis quality control will be discussed.
CORBEL (http://www.corbel-project.eu) is an initiative of eleven new biological and medical research infrastructures (BMS RIs), which together will create a platform for harmonised user access to biological and medical technologies, biological samples and data services required by cutting-edge biomedical research. CORBEL will boost the efficiency, productivity and impact of European biomedical research.
This webinar took place on 11th April 2019 and is part of the CORBEL webinar series. A recording of the webinar is available through the CORBEL website:
https://www.corbel-project.eu/webinars/bbmri-eric-quality-management-services.html
For previous and upcoming CORBEL webinars see:
http://www.corbel-project.eu/webinars
4. BACKGROUND
4
Since 2015, thirteen ESFRI Research Infrastructures from the field of
BioMedical Science (BMS RI) joined their scientific capabilities and
services to transform the understanding of biological mechanisms
and accelerate its translation into medical care.
• biobanking & biomolecular
resources
• curated databases
• marine model organisms
• systems biology
• translational research
• functional genomics
• screening & medicinal
chemistry
• microorganisms
• clinical trials
• structural biology
• biological/medical imaging• plant phenotyping
• highly pathogenic
microorganisms
5. CORBEL MISSION
5
Modern biological and biomedical research involves complex projects and a variety of
different technologies.
Some of the most important discoveries are made at the interface between different
disciplines.
CORBEL will harmonise access and services for complex research projects
involving more than one RI that offer:
• biological and medical technologies
• biological samples and
• data services
6. TODAY’S PRESENTER
11/04/2019 6
ChristianTischer studied physics in Heidelberg,
followed by PhD at EMBL with Philippe Bastiaens
working on microscope development and
signalling in mammalian cells. Subsequently, he
did a postdoc with Marileen Dogertom at AMOLF
in the Netherlands working on microtubule
dynamics.
From 2009 until 2018, he worked at EMBL's Advanced Light
Microscopy Facility (ALMF) supporting scientists with both
microscopy and image analysis. Since end of 2018, Christian’s
focus shifted completely towards image analysis support and he is
now running EMBL’s Centre for Bioimage Analysis (CBA).
8. Bioimage Analysis
Automatically extract biophysically meaningful
information from microscopy images of biological
samples.
Bioimage Analyst
EU funded action: https://www.cost.eu/actions/CA15124
Network of European Bioimage Analysts: www.neubias.org
12. Image Data Type Conversions
● Lower bit depth => Higher bit depth
○ e.g. 8-bit to 16-bit
○ usually preserves pixel values
● Higher bit depth => Lower bit depth
○ e.g. 16-bit to 8-bit
○ often deteriorates pixels values
21. Multi-class Segmentation
of Electron Microscopy Data
process
Mitochondria
Other
Cytoplasm
process
process
process
threshold
threshold
threshold
threshold
22. Machine Learning for Image Segmentation
threshold
threshold
threshold
threshold
threshold
Arganda-Carreras, I., et al. (2017) Bioinformatics 33(15):2424-2426;
Sommer, C., et al. (2011) doi: 10.1109/ISBI.2011.5872394;
Ronneberger O., et al. (2015) doi: 10.1007/978-3-319-24574-4_28
edge
average
...
...
...
...
...
...
...
threshold
threshold
threshold
threshold
29. Thank you!
What
questions
do you have?
Thanks for input and data:
Advanced Light Microscopy Facility (EMBL),
Pepperkok Lab (EMBL), Volker Hilsenstein (Monash
University), Kota Miura (NEuBIAS), Ellenberg Lab
(EMBL), Schwab Lab (EMBL), , Kreshuk Lab
(EMBL), Jason Swedlow (Univ. Dundee), Anne
Carpenter (Broad Institute),
The www.image.sc community and many more...
30. Questions?
A Basic Introduction to Bioimage Analysis
Presenter: ChristianTischer (Centre for Bioimage Analysis (CBA), EMBL)
11/04/2019
Please write your questions in the questions
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