Arne Seitz

Biography

04/1996-06/2000 Scientific co-worker at Philipps-University of Marburg, Dep. of Physical Chemistry

07/2000-10/2002 Post Doc at Max-Planck Unit for Structural Molecular Biology in Hamburg

11/2002-11/2005 Post Doc at European Molecular Biolohy Laboratory (EMBL), Cell Biology and Cell Biophysics Programme

11/2005-03/2009 Staff Scientist at Advanced Light Microscopy Facility, EMBL

04/2009- Head of Bioimaging and Optics platforme (BIOP), Ecole Polytechnique Fédérale de Lausanne (EPFL)

Official source

https://people.epfl.ch/arne.seitz

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Related publications (19)

MarrowQuant 2.0: A Digital Pathology Workflow Assisting Bone Marrow Evaluation in Experimental and Clinical Hematology

Giovanna Ambrosini, Olivier Burri, Mariangela Costanza, Bart Deplancke, Olaia Maria Naveiras Torres-Quiroga, Rita Sarkis, Frédérica Schyrr, Arne Seitz, Martin Weigert

2023

An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix

Olivier Burri, Nicolas René Chiaruttini, Romain Guiet, Arne Seitz, Jessica Sordet-Dessimoz

Image analysis workflows for Histology increasingly require the correlation and combination of measurements across several whole slide images. Indeed, for multiplexing, as well as multimodal imaging, it is indispensable that the same sample is imaged multiple times, either through various systems for multimodal imaging, or using the same system but throughout rounds of sample manipulation (e.g. multiple staining sessions). In both cases slight deformations from one image to another are unavoidable, leading to an imperfect superimposition Redundant and thus a loss of accuracy making it difficult to link measurements, in particular at the cellular level. Using pre-existing software components and developing missing ones, we propose a user-friendly workflow which facilitates the nonlinear registration of whole slide images in order to reach sub-cellular resolution level. The set of whole slide images to register and analyze is at first defined as a QuPath project. Fiji is then used to open the QuPath project and perform the registrations. Each registration is automated by using an elastix backend, or semi-automated by using BigWarp in order to interactively correct the results of the automated registration. These transformations can then be retrieved in QuPath to transfer any regions of interest from an image to the corresponding registered images. In addition, the transformations can be applied in QuPath to produce on-the-fly transformed images that can be displayed on top of the reference image. Thus, relevant data can be combined and analyzed throughout all registered slides, facilitating the analysis of correlative results for multiplexed and multimodal imaging.

FRONTIERS MEDIA SA2022

Biotin-NeutrAvidin Mediated Immobilization of Polymer Micro- and Nanoparticles on T Lymphocytes

Maxime Ayer, Olivier Burri, Romain Guiet, Harm-Anton Klok, Arne Seitz

Cells are powerful carriers that can help to improve the delivery of nanomedicines. One approach to use cells as carriers is to immobilize the nanoparticulate cargo on the cell surface. While a plethora of chemical conjugation strategies are available to bind nanoparticles to cell surfaces, only relatively little is known about the effects of particle size and cell type on the surface immobilization of nanoparticles. This study investigates the biotin-NeutrAvidin mediated immobilization of model polymer nanoparticles with sizes ranging from 40 nm to 1 mu m on two different T cell lines, viz., human Jurkat cells as well as mouse SJL/PLP7 T cells, which are of potential interest for drug delivery across the blood-brain barrier. The nanoparticle cell surface immobilization and the particle surface concentration and distribution were analyzed by flow cytometry and confocal microscopy. The functional properties of nanoparticle-modified SJL/PLP7 T cells were assessed in an ICAM-1 binding assay as well as in a two-chamber setup in which the migration of the particle-modified T cells across an in vitro model of the blood-brain barrier was studied. The results of these experiments highlight the effects of particle size and cell line on the surface immobilization of nanoparticles on living cells.

2021