PhD Positions – NEXTSCREEN

Pos.#

Institute

Location

Contract Duration

Application Deadline

Status

Politecnico di Milano

Milano, Italy

3 Years

Jan 31^st 2024

Closed

Project Description

Build a novel light sheet fluorescence microscope, for imaging of single cells at ultra-high resolution and throughput.
Integrate the hardware control for image acquisition with real-time deconvolution, segmentation and classification of the recorded cells.
Promote open-source code (for acquisition and processing), and open hardware (for improving the reproducibility and standardization of the technology), contributing to the democratization of single cell screening technologies.

Topics

The candidate should have a Master degree in one of these disciplines:

Universitäts Medizin Essen

Essen, Germany

3-4 Years

Jan 31^st 2024

Closed

Project Description

Establish genetically engineered cells lines whose cells to release fluorescently labelled extracellular vesicles (EVs). Respective EVs should serve as reference material within the consortium and beyond.
For the scaled production of reference EVs, conditions for the cell expansion in a bioreactor need to be optimized. Also, the scaled preparation of EVs via filtration and chromatography based downstream methods needs to be optimized. For the distribution to the partners, storage conditions need to be also optimized, ideally allowing the distribution of lyophilized EV reference material.
Optimize antibody-based EV labelling protocols (especially the selection of suitable fluorophores-conjugate antibodies, their applied antibody concentrations and the possible combination of different antibodies) will be the basis for extensive characterization of EVs diagnostic potential with imaging flow cytometry.

Topics

The candidate should have a Master degree in one of these disciplines:

The Institute of Photonic Sciences

Barcelona, Spain

3-4 Years

Dec 20^th 2023

Closed

Project Description

Develop a new fluidic imaging system, using high resolution long working distance microscope objective lenses, integrated with non-diffractive beams for illumination. This will allow capturing high-resolution 3D images on a large field of view, recording hundreds-cells/s.
Develop an illuminator based on an optical lantern (patented at ICFO) to generate incoherent light source compatible with light sheet illumination of elastic scattering as a source of contrast mechanism (avoiding shadowing effects typical of coherent illumination)

Apply here for this position: https://jobs.icfo.eu/?detail=866

Topics

The candidate should have a Master degree in one of these disciplines:

Consiglio Nazionale delle Ricerche

Milano, Italy

3 Years

Jan 31^st 2024

Closed

Project Description

Develop novel integrated system with optical and fluidic components for cellular imaging.
Fabricate an integrated structured light generator based on the integrated directional couplers, Mach-Zehnder interferometers and phase-shifters on chip. The integration would allow reaching high stability in the optical phase modulation and light polarization to be used in miniaturized microscopes.
Design an array of miniaturized lenses for image detection in the IFC chip. This will demonstrate the feasibility of a fully integrated optofluidic device that combines illumination detection and sample scanning.

Topics

The candidate should have a Master degree in one of these disciplines:

University of Crete

Heraklion, Greece

3 Years

Jan 31^st 2024

Closed

Project Description

Characterize low refractive index plastics from the physical and cytotoxic standpoints
Develop microfluidics devices prototyped with 2-photon polymerization, made of inert, non-toxic plastic material, having refractive index close to the one of the cells (water, PDS, culture media)
Setup a protocol for plastic chip printing. These devices will be a powerful alternative to Polydimethylsiloxane (PDMS) to be used in microscopy settings, matching the refractive index of the sample thus avoiding optical aberrations.

Topic

The candidate should have a Master degree in this discipline:

Universitat Politècnica de València

Valencia, Spain

3-4 Years

Jan 31^st 2024

Closed

Project Description

Design and develop the end-to-end algorithm for the real-time cell detection-segmentation, taking into account the availability of the labels.
Design and implement a style transfer-based system that will allow converting from one domain to another (fluorescence-brightfield, 2D-3D) in a bidirectional way.
Investigate and develop a weakly-supervised deep-learning algorithm based on IFC data for binary classification in normal or diseased cells.

Topic

The candidate should have a Master degree in this discipline:

Universität Tübingen

Tübingen, Germany

3-4 Years

Jan 31^st 2024

Closed

Project Description

Develop a deep encoder-decoder models for the reconstruction of fluorescence/deformability imaging flow cytometry data.
Develop a weakly supervised machine learning model for peripheral blood mononuclear cells (PBMC) measurements associated with weak labels from fluorescence measurements.

Topic

The candidate should have a Master degree in this discipline:

Eidgenössische Technische Hochschule Zürich

Zürich, Switzerland

3-4 Years

–

Closed

Project Description

Distinguish normal lymphocytes distinguished from malignant or reactive lymphocytes (e.g., viral infection) from deformability imaging of peripheral blood mononuclear cells (PMBC).
Demonstrate specific B-cell leukaemia (CLL) detectability, based on deformability imaging without using conventional antibody-based flow cytometry
Evaluate single-cell deformability metrics and the definition of disease-specific deformability signatures from clinical samples.

Topics

The candidate should have a Master degree in one of these disciplines:

Elvesys – Microfluidics Innovation Center

Paris, France

3 Years

Apr 30^th 2024

Closed

Project Description

Development and implementation of closed loop microfluidic circuits for new generation Imaging Flow Cytometry, including instrumentation surpassing the state-of-the-art with high precision pressure control for the delivery of cell samples in suspension
Development of a microfluidic system for flow-through surface functionalization of microdevices with novel polymers having refractive index matching that of water.
For more details on the job offer, please visit the company website.

Topics

The candidate should have a Master degree in one of these disciplines:

Abbelight

Paris, France

3 Years

May 15^th 2024

Closed

Project Description

Test the feasibility of structured illumination microscopy and modulated localisation microscopy for pushing the resolution of cellular imaging to the limit
Investigate and develop a computational strategy based on artificial neural networks to speed up the reconstruction processing needed for super-resolution images from both sparse, acquired localization images and structured illumination images.
Develop an algorithm, for correction of sample vibration/translation in the fluid stream. Correcting drift is a fundamental challenge in IFC, that would generate high impact results, even beyond the applications of the project.

Topics

The candidate should have a Master degree in one of these disciplines:

Politecnico di Milano

Milano, Italy

3 Years

March 31^st 2024

Closed

Project Description

Develop a novel workflow for peripheral blood mononuclear cells isolation, labeling and injection in microfluidics systems for high throughput imaging.
Investigate the morphology of blood cells, aided by deep learning for cell labelling and classification.

Topics

The candidate should have a Master degree in one of these disciplines:

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Project coordinator: Andrea Bassi

Project manager: Giorgia Lancerotti

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