Biomedical Image Analysis Beginner
In this introductory image analysis course, we will use the open-source image analysis Fiji 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.
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Is this course for me?
This course is targeted at anyone working with microscopy and/or visual data. This course is the ideal choice if you are just getting started with your image analysis journey.
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Learning targets:
(1) Understanding Data: Understand how 3D data are constructed and what image properties are important in optical fluorescence microscopy.
(2) Image Analysis: Examine and visualize 3D images, understand image properties, and the usefulness of LUTs. Common image analysis steps such as data understanding, image enhancement, segmentation, and quantification.
(3) Hands-on: Using hands-on exercises will provide the attendees with a broader understanding of quantitative image analysis. Attendees will be provided with workbooks as well as real-life data.
(4) Long-term: The tutorial is designed to be interactive with attendees assessing the learned principles.
Biomedical Image Analysis Intermediate
Participants will use the open-source software Fiji to enhance, segment, and quantify provided 3D data. This includes steps such as optimizing segmentation, skeletonization methods, 3D volumetric analysis. The course includes a one-hour lecture followed by a three-hour hands-on tutorial with practical examples to illustrate advanced workflows and discuss broader implications.
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Is this course for me?
For this course, participants are expected to have an understanding about multi-dimensional microscopy data and basic Fiji proficiency. If you are unsure, we can also offer a bundle with the beginner course.
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Learning targets:
(1) Advanced Data Understanding: Delve deeper into 3D data analysis with a focus on optical fluorescence microscopy, emphasizing complex data interpretation and problem-solving.
(2) Comprehensive Image Analysis: Explore advanced image analysis techniques, including sophisticated data understanding, enhancement, segmentation, and quantification methods. This includes steps such as optimizing segmentation, skeletonization methods, 3D volumetric analysis.
(3) Practical Application: Engage in intensive hands-on exercises designed to deepen your understanding and proficiency in quantitative image analysis.
(4) Reflective Learning: After each tutorial step, participants will have time to reflect on their learning to appreciate the broader implications and applications of the techniques covered. In addition, we will pay attention to how the learned can be used in practice by the attendees by their own data. ​
Biomedical Image Analysis Advanced
In this advanced image analysis course, participants will use the open-source software Fiji and Python to enhance, segment, and quantify provided 3D data. We will use heavily look into code, automation, and how to compare and improve image analysis results. The course includes a one-hour lecture followed by a three-hour hands-on tutorial with practical examples to illustrate advanced workflows and discuss broader implications.
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Audience: This course is for advanced image analysis users and require sufficient prior knowledge of attendees. Ideally, all participants are versed with multi-dimensional image analysis and bring some coding experience with them. This course will also look at specific applications, so if you have data you would like to explore, please reach out to us before the course starts. If unsure, a bundle with the beginner or intermediate course is available.
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(1) Advanced Data Understanding: Lets take a deep dive into 3D data analysis and complex data interpretation and problem-solving. This course will require prior knowledge on 3D images construction and general image processing (such as filters and segmentation).
​(2) Comprehensive Image Analysis:​ Optimize segmentation, apply skeletonization methods, and conduct 3D volumetric analysis (exploration of different methods and Plugins). We will also cover the automation of multi-dimensional data analysis and Macro scripting. In addition, we will compare Macro scripting in Fiji with Python for automating and enhancing image analysis workflows.​
(3) Practical Application: Engage in intensive hands-on exercises designed to deepen your understanding and proficiency in quantitative image analysis. Work with real-world datasets to practice and refine skills. Enhancing and analyzing 3D+ images of live cell processes using both Fiji and Python scripts.
(4) Reflective Learning: Discuss the generalization and application of techniques to various types of microscopy data. Evaluating the scalability and efficiency of different image analysis methods.​
Exceptional Quality for Your Continuous Professional Development
All training is overseen by our director Dr Elisabeth Kugler, who is:
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The CPD Group accredited trainer #405290
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Associate Fellow (AFHEA) #PR221380 against the UK Professional Standards Framework for teaching and learning support in higher education
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Member of the Royal Society of Biology, fulfilling a minimum of 50 CPD credits annually for the CPD scheme
