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:
Computer sciences
Biomedical Engineering
Electronic Engineering
Optical Engineering
2
Universitäts Medizin Essen
Essen, Germany
3-4 Years
Jan 31st 2024
Closed
Project Description
Establish genetically engineered cells lines whose cellsto 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:
Biology
Biotechnology
Medicine
3
The Institute of Photonic Sciences
Barcelona, Spain
3-4 Years
Dec 20th 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)
The candidate should have a Master degree in one of these disciplines:
Biomedical Engineering
Optical Engineering
Electronic Engineering
Computer sciences
4
Consiglio Nazionale delle Ricerche
Milano, Italy
3 Years
Jan 31st 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:
Optical Engineering
Electronic Engineering
Chemistry and Material sciences
5
University of Crete
Heraklion, Greece
3 Years
Jan 31st 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:
Chemistry and Material sciences
6
Universitat Politècnica de València
Valencia, Spain
3-4 Years
Jan 31st 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:
Computer sciences
7
Universität Tübingen
Tübingen, Germany
3-4 Years
Jan 31st 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:
Computer sciences
8
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:
Biomedical Engineering
Optical Engineering
Electronic Engineering
Chemistry and Material sciences
Computer sciences
9
Elvesys – Microfluidics Innovation Center
Paris, France
3 Years
Apr 30th 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.
The candidate should have a Master degree in one of these disciplines:
Biochemistry
Chemistry
Cell biology
Engineering (bioengineering, mechatronics, robotics, engineering physics etc.) or related fields
10
Abbelight
Paris, France
3 Years
May 15th 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:
Computer sciences
Optical Engineering
11
Politecnico di Milano
Milano, Italy
3 Years
March 31st 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: