Skip to content

Guest Presentation: New Framework for Stem Cell Analysis

Dortmund, 27th January 2023

Understanding and predicting the behaviour of cells in normal, regenerative and pathological contexts – these are the goals of the Allen Institute for Cell Science. To achieve this, the non-profit research organisation develops multi-scale visual models of cell organisation, dynamics and activity. Its software programmes are freely accessible to researchers worldwide (open source). They are part of the Allen Cell Explorer, a portal for cells, cell biology, data and tools. The portal provides insight into the organisational diversity of human stem cells and delivers matching open data, cell lines, plasmids and models. Human stem cells from the test tube, so-called induced pluripotent stem cells, are the subject of a recently published paper in Nature.

How does a subset of expressed genes dictate cellular phenotype – the visible properties of cells? Finding the answer to this question is a considerable challenge for scientists due to the large number of molecules involved, their combinatorics and the abundance of cellular behaviors that determine this phenotype. Scientists at the Allen Institute for Cell Science have recently succeeded in developing a framework for the analysis of integrated intracellular organization and its variations in human iPS cells, based on datasets of 200,000 living cells in 3D and a set of 25 key structures.

 A framework is a basic software scaffold that developers can use to build computer applications. The framework developed at the Allen Institute for Cell Science allows for programming analysis software that converts raw image data of iPS cells and their structures into dimensionally reduced, quantitative analyses.

Portrait Susanne Rafelski.

Dr Susanne Rafelksi is a biochemist and has been Deputy Director of Scientific Programmes at the Allen Institute for Cell Science since 2020.

How the framework will exactly advance stem cell analysis is the topic of Dr. Susanne Rafelski's presentation, “Integrated intracellular organization and its variations in human iPS cells,” at ISAS on February 7.

Tuesday, February 7
10.30 am
Webex

https://t1p.de/rk032
Meeting ID: 2730 175 0712
Password: uMegm3Dw5B5

Rafelski is deputy director of scientific programmes at the Seattle institute – and corresponding author of the Nature publication. ISAS has a cooperation with the Allen Institute for Cell Science. The AMBIOM working group led by Dr Jianxu Chen is in charge here. The 34-year-old worked at the Allen Institute for Cell Science for four years before joining ISAS.

(Sara Rebein)

Share

Further articles

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.
12th March 2025

Two-step Analysis is a Thing of the Past Thanks to Innovative Mass Spectrometry

Fast and accurate mass spectrometric detection of non-polar substances such as cholesterol together with polar substances? And in just one analysis run? This is made possible by a new combination method that unites two ionization sources in one setup.

Daniel Foest steht im Labor und hält ein Papier mit einer Leberprobe, die er am Massenspektrometer untersucht.
10th March 2025

University professorship (W3) in “New Analytical Methods for Precision Medicine”

ISAS and the University of Duisburg-Essen are strengthening their existing collaboration with a further professorship based on the Jülich model. Applications are possible until April 6, 2025.

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.
14th February 2025

Valentines’ Day: Perfect Couples in the Lab

On Valentine's Day, the editors of ISAS Kompakt wanted to know what makes our researchers' hearts beat faster. The examples from the laboratories of the Bioimaging and NMR Metabolomics research groups show that special bonds do not only exist in love, but also in science.

Porträt von Dr. Themistoklis Venianakis.
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.
28th January 2025

A Small But Very Important Step

Susmita Ghosh joined the Biofluorescence research group at ISAS in October 2021. The PhD student has now received the first funding of her career for her pilot project “Dissecting the neutrophil-tumor cell interactome using SILAC-labelling”.

Portrait Susmita Ghosh.
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.
15th January 2025

Dorit Günther appointed to the ISAS Executive Board

Günther will assume the role of Chief Financial Officer of ISAS.

Portrait von Dorit Günther.