Oliver Stein joins the HASTE team to work on intelligent operators placement and auto-scaling in streaming frameworks

Oliver’s MSc thesis will investigate intelligent ways to manage and position docker containers in a VM environment, in order to improve efficiency in physical resource usage and maintain performance. The implementation of such a controller system will be developed in coordination with the HarmonicIO streaming framework used in HASTE, which will help the automatic scaling of containers working in the system as well as evaluate the design with a real use case.

Phil Harrison joins the HASTE team to work on predictive modeling with confidence

We welcome Phil Harrison as new PhD Student in the Spjuth lab. Phil obtained his first PhD in marine biology in 2006 studying the population dynamics of grey seals. Between 2006-2016 he undertook several research projects modelling wildlife populations and analysing trends in biodiversity. In the HASTE project, Phil  will develop machine learning methods for online, large-scale analysis of microscopy image data based on statistical earning including e.g. conformal prediction and probabilistic prediction.

Ben Blamey joins the team to work on intelligent cloud services

We are nearing the end of an intensive recruitment period, looking for excellent established and emergent scientists to help us realize the goals of this interdisciplinary project.

This week we are very pleased to welcome Dr. Ben Blamey to the team. He will work in the Hellander lab, in close collaboration with Dr.  Salman Toor, and focus on computer science challenges in designing and developing smart and efficient systems for managing scientific data, and image data in particular, in distributed computing infrastructure such as  hybrid and fog cloud.

With a background on research in machine learning, natural language processing and in development of services in cloud infrastructure both in academia and in industry, Dr. Blamey brings critical experience to the team.

In the featured image Dr. Blamey (right) is busy discussing a potential design of an intelligent system to manage information hierarchies in distributed environments with Dr. Toor (left).

Håkan Wieslander starts a PhD position

We are happy to welcome Håkan Wieslander to the team and to PhD education at the department of Information Technology, Uppsala University!

Håkan grew up in Lund, Sweden and moved to Uppsala 2011 to study Engineering Physics. In 2017 he obtained a masters degree in computational science. The MSc thesis was about classification of malignant cells using deep learning. 

About the PhD project within HASTE:  

Collection of large amounts of data often results in high-quality, highly informative data intermixed with data that is either of poor quality or of little interest in relation to the question at hand. Wieslander’s thesis work will focus on development of computationally inexpensive measurements that will identify non-informative data early on in the analysis process; either online at data collection, or off-line prior to full data analysis. The challenge is to use minimal computational time and power to extract a broad range of informative measurements from spatial-, temporal-, and multi-parametric image data, useful as input for conformal predictions and efficient enough to work well in a streaming setting. 

Visit to AstraZeneca to learn about high-content imaging workflows

Lovisa Lugnegård, working with Andreas Hellander and Carolina Wählby, is working towards a cloud-based simulator of the data generation of high-content imaging experiments.  She recently visited Alan Sabirsh and Johan Karlsson at AstraZeneca to learn about their microscopy pipelines and about what parameters are important for the rate of data produced in experiments, as well as to collect an example dataset to drive her development.

Johan teaches Lovisa about their Image Express microscope, to figure out how different settings affect the resulting images.

Lovisa Lugnegård writes her MSc thesis as part of the project

We are happy to welcome Lovisa Lugnegård to the team! Lovisa will write her MSc thesis within the project. She plans to design and prototype a cloud-based simulator capable of streaming already generated microscopy data, varying a wide range of parameters and emulating realistic scenarios when running high-content imaging platforms. This will be a valuable tool for quick prototyping of new algorithms, and for mapping out e.g. performance requirements for feature extraction methods in real-time scenarios.