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The aim of the junior research group AMBIOM – Analysis of Microscopic BIOMedical Images, which is funded by the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF), is to enable a high analytical throughput of microscopic images. The research group plans to develop algorithms and methods (open source) by 2026 that will allow countless image data worldwide to be analysed automatically, quickly and economically.

© ISAS / Hannes Woidich

Focus: large 3D microscopy imaging data

The research group concentrates on the development of scalable AI-based biomedical image analysis algorithms, particularly for large 3D microscopy image data. AMBIOM’s work aims to allow broad-based new studies on the development of diseases and their consequences at the level of entire organs and organ systems. Furthermore, the AI analysis methods developed at ISAS are intended to help doctors in making diagnostic and therapeutic decisions.

The MSCoreSys associated junior research group AMBIOM – Analysis of Microscopic BiOMedical Images is funded by the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF) under the funding reference 161L0272.

Highlights

24th January 2024

EfficientBioAI: New Open-Source Software Makes AI Models Lighter and Greener

Artificial intelligence has become an integral part of research. However, the better and more complex the models become, the higher their energy consumption. Researchers at ISAS and Peking University have therefore developed ready-to-use and open software that compresses existing bioimaging AI models. With the help of the new toolbox, scientists can now run their models faster and with significantly lower energy consumption.

Die Abbildung zeigt die 3D-Semantiksegmentierung von Osteozyten in Mäuseknochen vor und nach der Kompression des Modells mir EfficientBioAI Die Bilder wurden mittels Lichtblatt-Fluoreszenzmikroskopie aufgenommen.
30th April 2025

Humboldt Fellow Prof Dr Xiaowei Xu started at ISAS in March

Prof Dr Xiaowei Xu from the Chinese Guangdong Cardiovascular Institute is researching the clinical application of artificial intelligence (AI) in the context of cardiovascular diseases. For 18 months in total, he will be researching various AI methods for analysing cell images as a Humboldt Fellow at ISAS.

Prof Dr Xiaowei Xu in front of the ISAS city building.
27th March 2025

Valuable Connections: Dr Jianxu Chen

Dr Jianxu Chen leads the junior research group AMBIOM - Analysis of Microscopic BIOMedical Images at ISAS since 2021. He previously worked at the Allen Institute for Cell Science in Seattle, USA. In the ISAS -Kompakt series ‘Valuable Connections’, the computer scientist reports on his move to health research and to Germany.

Portrait von Dr.  Jianxu Chen.
26th February 2025

What are you doing at ISAS, Leon?

What do marshmallows and chocolate have to do with cell analysis? Leon is finding out the answer during his school internship at ISAS. For ISAS Kompakt, the 15-year-old talks about what else he is learning during his time at the institute.

Leon hält Marshmallows, Schokolade und die Hardware für sein Projekt zur Bilderkennung.
4th February 2025

Valuable Connections: Adrian Sebuliba

Adrian Sebuliba joined the ISAS junior research group AMBIOM in 2023 as a software engineer. Previously, he worked for a digital commerce platform for the chemical industry in Uganda. In the ISAS Kompakt series ‘Valuable Connections’, he reports on his move into health research, among other things.

Portrait of Adrian Sebuliba.
17th January 2025

What are you doing at ISAS, Lennart?

What fascinates you about your work as a software engineer? And why are you engaged in the works council? Lennart Kowitz answers these and other questions in ISAS Kompakt.

Portrait of Lennart Kowitz.
10th December 2024

Xiaowei Xu Will Join ISAS as a Humboldt Fellow

As a fellow of the Alexander von Humboldt Foundation, Prof Dr Xiaowei Xu will be conducting research at ISAS from February 2025. In this interview, he talks about his work on artificial intelligence in health research and what he plans to do in Dortmund.

Portrait of Prof Dr Xiaowei Xu.
21st November 2024

PODCAST »NACHGEFORSCHT – DIE LIVESCHALTE INS LABOR« Episode 10: Resource Awareness in Biomedical Image Analysis

Dr Jianxu Chen heads the junior research group AMBIOM - Analysis of Microscopic BIOMedical Images at ISAS. In the first English-language episode of »NACHGEFORSCHT - DIE LIVESCHALTE INS LABOR«, he talks about his path from mathematics to the life sciences and how he wants to make the analysis of biomedical data more sustainable - on many levels.

8th November 2024

Using the Russian Doll Principle to Analyse Biological Structures

In the “AI-assisted imaging of large tissues” project, several ISAS research groups are working on combining various microscopic and mass spectrometric methods. Much like looking at a Russian doll, the team looks deeper into the biological structures of a sample with each step.

Flora Weber at the lightsheet fluorescence microscope.
31st October 2024

AI in Healthcare: Why Is it Better to Think Small Instead of Big?

Sustainability is an important topic when it comes to artificial intelligence in health research. A group of international researchers, including from ISAS, has been working on this topic and published a Perspective in Nature Machine Intelligence. In the interview, Prof Dr Yiyu Shi talks about the resource problem and possible solutions.

Portrait von Prof. Dr. Yiyu Shi.

Projects

AI Assisted Imaging of Large Tissues

Researchers on the »Imaging of Large Tissues« project are developing a workflow to combine the various microscopy imaging methods and analytical, mass spectroscopy methods.

Biochemical Annotations of Mass Spectrometry Imaging Data for Worldwide Exchange

The research groups AMBIOM and Spatial Metabolomics are working together to develop a plug-in for the multi-dimensional imaging software napari that makes it possible to visualise and biochemically annotate MSI data.

Creating 'Leibniz Mass Spectral Imaging Library' for Identification of Primary & Secondary Metabolites

The project aims at creating the first-ever open-access MSI library of over 1000 bioactive compound standards on different matrix-assisted laser desorption/ionization (MALDI) MSI platforms.

Smart Human-in-the-loop Segmentation

Scientist working on the project »Smart Human-in-the-loop Segmentation« aim to develop a powerful deep learning model that is trained with a minimum amount of human effort.

Cell Tracking in Microscopy Images

The research project »Cell Tracking in Microscopy Images« aims to develop new sophisticated cell detection and tracking algorithms to tackle some of the most challenging tracking problems.

Team

Dr. Jianxu Chen

Research Group Leader

Department: Biospectroscopy

Research group: AMBIOM

Portrait von Dr.  Jianxu Chen.

Lennart Kowitz

IT system administrator

Department: Biospectroscopy

Research group: AMBIOM

Portrait von  Lennart Kowitz.

Dr. Peter Lampen

Research Associate

Department: Biospectroscopy

Research group: AMBIOM

Davide Panzeri

Research Associate

Department: Biospectroscopy

Research group: AMBIOM

Simon Püttmann

Research Associate

Department: Biospectroscopy

Research group: AMBIOM

Justin Sonneck

Research Associate

Department: Biospectroscopy

Research group: AMBIOM

Portrait von  Justin  Sonneck.

Jonathan Jair Sánchez

Research Associate

Department: Biospectroscopy

Research group: AMBIOM

Shuo Zhao

Research Associate

Department: Biospectroscopy

Research group: AMBIOM

Portrait von  Shuo Zhao.

Yu Zhou

Research Associate

Department: Biospectroscopy

Research group: AMBIOM

Portrait von  Yu Zhou.