Mission
Microscopy and image analysis are so strongly intertwined that it is impossible to talk about one without the other. We aim to form an international network among young scientists in which we can discuss our specific imaging and analysis issues in an informal, peer- based environment. We offer problem- based learning on flexible, on-demand topics (watch parties of online lectures, roundtable discussions and troubleshooting sessions), as well as events with invited experts. Participation in the YMIA network is supported by GerBI, but does not require a GerBI membership.
Join the YMIA Watchparty on 30.04.2024 at 4pm about “Image Filtering and Segmentation” to learn about the basic principles of image processing: Sign up for the Watchparty Event Series!
Upcoming Events
For our next event series, we delve into Bioimage Analysis! Across 14 weeks, we’ve curated a watchparty series featuring Robert Haase’s recorded lectures on Bioimage Analysis (https://www.youtube.com/playlist?list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U), covering fundamental principles, filtering, segmentation, feature extraction, macro programming in Fiji, Tracking with Trackmate, machine learning with Fiji and Ilastik, and image registration. The series includes “software playground” sessions to apply learned concepts to microscopy data, though not every week. For additional events, reach out and share your interest! Get the links and stay informed by signing up to the event series.
| Date | Time | Event | Topic |
|---|---|---|---|
| 30.04.2024 | 4pm – 5:30 CEST | Watchparty | 2a Image Filtering and Segmentation 2b Image Filtering and Segmentation with Fiji |
| 07.05.2024 | 4pm – 5:30 CEST | Watchparty | 3a Feature Extraction 3b Introduction to ImageJ Macro Programming: Variables and Operations 3c ImageJ Macro programming: Recording Macros and working with images |
| 14.05.2024 | 4pm – 5:30 CEST | Watchparty | 3d ImageJ Macro programming: Conditions and loops 4a ImageJ macro programming: ROIs and Overlays |
| 21.05.2024 | 4pm – 5:30 CEST | Watchparty | 4b ImageJ macro programming: Functions, Arrays, Plots and Tables 4c ImageJ macro programming: User interfaces |
| 23.05.2024 | 4pm – 5:30 CEST | Software Playground |
Let’s apply our newfound knowledge to our own data; everyone brings their own dataset to extract meaningful insights, with Rike on hand to troubleshoot and offer advice on diverse analysis approaches. |
| 28.05.2024 | 4pm – 5:30 CEST | Watchparty | 5a Bioimage Analysis with Cell Profiler 5b Bioimage Analysis with KNIME Image Processing 5c Bioimage Analysis with Icy Bioimaging |
| 30.05.2024 | 4pm – 5:30 CEST | Software Playground | Are you interested in trying CellProfiler, KNIME and/or Icy? Let’s try it together! |
| 04.06.2024 | 4pm – 5:30 CEST | Watchparty | 7a Spot detection and Tracking 7b Trackmate |
| 06.06.2024 | 4pm – 5:30 CEST | Software Playground |
Want to try tracking with Trackmate using your own data? Join this event for hands-on experience, with Rike available for troubleshooting and guidance in various settings. |
| 11.06.2024 | 4pm – 5:30 CEST | Watchparty | 8a Machine Learning for Pixel and Object Classification |
| 18.06.2024 | 4pm – 5:30 CEST | Watchparty | 8b Machine learning for pixel classification in Fiji 8c Machine learning for pixel and object classification in Ilastik |
| 20.06.2024 | 4pm – 5:30 CEST | Software Playground | Do you want to try pixel classification with your own data? Join this event to test Labkit in Fiji or Ilastik. Rike will be there to help out if something doesn’t work, or to give some advice in different settings. |
| 25.06.2024 | 4pm – 5:30 CEST | Watchparty | 12a Volumetric Image Processing 12b 3D Image Visualisation in Fiji 12c 3D image Processing in Fiji |
| 02.07.2024 | 4pm – 5:30 CEST | Watchparty | 13a Multi-dimensional Image Processing 13b Multi-dimensional Image Processing in Fiji |
| 09.07.2024 | 4pm – 5:30 CEST | Watchparty | 14a Image Registration 14b Image Registration in Fiji |
| 16.07.2024 | 4pm – 5:30 CEST | Watchparty | 14c Applied Bioimage analysis Lecture 2020 – A summary |
| 18.07.2024 | 4pm – 5:30 CEST | Software Playground | Let’s come together and combine our knowledge for image processing to tackle our own image analysis needs. Bring your data and get it on with the coding! Rike will be there to help out if something doesn’t work, or to give some advice for different analysis approaches. |
| 23.07.2024 | 4pm – 5:30 CEST | Watchparty | GPU Accelerated Image Processing with CLIJ2 – Webinar |
| 25.07.2024 | 4pm – 5:30 CEST | Software Playground | Are you curious how CLIJ2 could be used in your own image analysis pipelines? Let’s try to implement this tool for our own data! Rike will be there to help out if something doesn’t work, or to give some advice for different analysis approaches. |
Activities
Watch parties
Watch-Parties are a communal way to follow prerecorded lecture series in the YMIA. This way you can update your knowledge in varying fields of microscopy and image analysis applications in an interactive way together with your peers and discuss questions afterwards.
Software Playground
Let’s code together! Experience interactive coding sessions where brainstorming and troubleshooting take center stage. Uncover solutions, overcome obstacles, and elevate your coding skills by interacting with the community.
Roundtable Discussion
Roundtable discussions are an opportunity to discuss issues, to connect, as well as to introduce yourself and your research.
Expert Session
Engage in Expert sessions featuring topics chosen by the YMIA community, presented by field-leading experts for insightful discussions and invaluable insights.
Resources
The resource database is a collection of knowledge that is deemed to be especially useful to young researchers. We focus on already existing other databases, as well as literature and youtube videos that already exist on other platforms. We are also working on establishing a database on how to connect to other existing local networks – to core facilities or self-help services – to promote finding on-site support whenever possible.
Who we are
Core team
Team Members
- Sona Michlikova – PostDoc (Translational Radiooncology) at the National Center for Radiation Research in Oncology (OncoRay) in Dresden and Helmholz-Zentrum Dresden – Rossendorf
- Friederike Kessel – PostDoc at the Center for Regenerative Therapies Dresden, Neural Development and Regeneration
- Annika Haak – PhD Student (Biochemistry) at the RUBION, Ruhr-University Bochum
- Elena Nicolay, Research Assistant (M.Sc.) at UFZ Helmholtz Centre for Environmental Research Leipzig, Mechanistic Toxicology
With the help of a quick survey we assessed who was interested in the YMIA: Roughly 50% of the participants of this survey were PhD students, PostDocs and Master Students constitute the remaining half. Members of the team come from a variety of scientific backgrounds, including Biology, Physics, Engineering, Medicine and Bioinformatics. Their interests are equally distributed between both microscopy and image analysis.
Join the YMIA
Everyone is welcome to join, no matter where they are located or what imaging or analysis modality they are using. In order to join, please send an email to team-ymia@gerbi-gmb.de or sign up for the mailing list when you register for one of our events. If you are interested, you can also become an active member of the GerBI society, but this is not mandatory to join the online activities of the YMIA.
