Image analyst in 3D confocal microscopy in Zurich, Switzerland

We are looking for a highly motivated bioimage data analyst to join the lab of César Nombela-Arrieta, at the department of Medical Oncology and Hematology of the University (UZH) and University Hospital Zurich (USZ). Our research group employs cutting edge 3D imaging, single- cell technologies and in vivo mouse models to dissect novel aspects of the regulation of hematopoietic stem cells by the bone marrow microenvironment in specific anatomical niches. Our goal is to uncover novel molecular and cellular mechanisms orchestrating healthy and pathological hematopoiesis. A general description of the main research lines of the lab can be found in www.nombelaarrieta.com We are looking for a data analyst with expertise in 3D image analysis and strong data science skills to integrate in our group. The goal will be employ and further develop existing image analysis tools in the lab (see publications [2008.12380] Modality Attention and Sampling Enables Deep Learning with Heterogeneous Marker Combinations in Fluorescence Microscopy, [2101.11476] Utilizing Uncertainty Estimation in Deep Learning Segmentation of Fluorescence Microscopy Images with Missing Markers), for the analysis of spatial associations between tissue components in 3D multidimensional microscopy datasets (Gomariz et al. Nat Commun. 2018; 9: 2532).

Candidates should have proven expertise in scientific programming and data science, in particular in the use of python and libraries such as pandas, numpy and matplotlib. Expertise in machine learning will be highly valued, including knowledge of deep learning frameworks such as tensorflow and pytorch. Demonstrated experience in image analysis projects with customized or widely employed frameworks ( Fiji, Cellprofiler…) is required. We are looking for candidates with strong interpersonal skills to work in teams, fluidly communicate with biologists and a innovative drive to contribute to and shape the outcome of research projects.

We offer: an interdisciplinary, international and friendly environment, possibility to participate in defined and near-publication projects through collaboration with lab members but also relative freedom to initiate and explore own lines and establish new analysis tools. Through UZH/ETH and the vibrant image analysis community of Zurich, candidates will have access to continuing education and specialized courses related to image analysis. The group is embedded in, and supported by the department of Medical Oncology and Hematology, formed by several research labs focusing on crucial translational aspects of healthy and malignant hematopoiesis.

The contract duration is initially for 1 year (with possible extensions). Remuneration will be determined according to the salary scale of the UZH and USZ subject to personal qualifications. The starting date is May-June 2021 but can be agreed upon.

Please send your application with a brief motivation letter, CV and contact details of at least two references, to: Cesar.NombelaArrieta@usz.ch

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