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MSCA-DN eRaDicate - Development of a highly innovative label-free & deep-learning based analysis method: Histoplasmonic Tissue Cytometry

26 Mar 2024

Job Information

Organisation/Company
TissueGnostics GmbH
Department
Research & Development
Research Field
Computer science » Programming
Computer science » Other
Researcher Profile
First Stage Researcher (R1)
Country
Austria
Application Deadline
Type of Contract
Temporary
Job Status
Full-time
Offer Starting Date
Is the job funded through the EU Research Framework Programme?
HE / MSCA
Reference Number
eRaDicate-DC-TG
Marie Curie Grant Agreement Number
101119427
Is the Job related to staff position within a Research Infrastructure?
No

Offer Description

The Marie-Skłodowska Curie Doctoral Network: “Innovative Ligands for Nuclear Receptors to Eradicate Cancer Relapse”, (eRaDicate) funded by the European Community is recruiting 11 young researchers.

The doctoral candidates (DCs) will be trained not only to perform original and independent research on an internationally competitive level but also to develop creative, critical, and entrepreneurial mind-sets, to be prepared for a wide spectrum of career opportunities.

eRaDicate is a doctoral network that combines training and research in almost equal parts. The network is built around a community of leading researchers and all DCs will be part of this community through secondments, training schools, eRaDicate events, and conferences. The research will be performed at 8 universities (Medical University of Vienna, University of Santiago de Compostela, University of Wroclaw, Medical University of Warsaw, University of Warsaw, University of Birmingham*, Ben-Gurion University of the Negev, and Trinity College Dublin) and a company (TissueGnostics GmbH). The objective of the network is to understand the role of nuclear receptors, such as retinoic acid receptor (RAR) and vitamin D receptor (VDR), in cancer development and to design and synthesise highly innovative compounds targeting these receptors, to become therapies against cancer stem cell-driven relapse and metastasis. Furthermore, the DCs in the network will devise pre-formulation strategies for the compounds and develop a novel, deep learning-based cancer analysis and diagnostics method.

After having completed their studies and the eRaDicate programme, this innovative and multidisciplinary training will qualify this new generation of scientists not only for an academic career but also for working in the industry and beyond.

See also www.eradicate-project.eu for more details.

Note that all of the projects have their individual job advertisement. Candidates may apply for a maximum of TWO projects. The DCs will be employed by the host organization of the selected project and enrolled in the host organization’s or affiliated university’s PhD programme.

(* the University of Birmingham is an Associated Partner of eRaDicate. The project at UoB is funded by UKRI rather than the MSCA. The student in Birmingham will have the same access, to training events, rights within eRaDicate as the other DCs, etc.).

 

APPLICATION DEADLINE: 30.4.2024

We may accept applications after this date, until all positions are filled.

 

General job description

  • manage and carry out the individual research project;
  • participate in the eRaDicate training and network activities;
  • take PhD courses;
  • write scientific articles and the PhD thesis;
  • participate in national and international congresses and scientific meetings;
  • research stay at external research laboratories or company sites;
  • disseminate the research outcomes;
  • participate in the undergraduate teaching of students.

 

Research project: Development of a highly innovative label-free & deep-learning based analysis method: Histoplasmonic Tissue Cytometry

The DC will perform applied research in bioinformatics, i.e., the extraction of numerical values from biological samples, by engaging deep learning technologies to microscopic images with the aim to develop a novel solution for future clinical diagnostics of cancer.

To develop algorithms that allow to extract diagnostic and prognostic information from label-free images of tumor samples on specific nanoparticle coated slides

  • The DC will develop experimental algorithms using deep-learning technologies for analysis of human and/or mouse cancer tissue.
  • The DC will develop and execute a test plan comparing to visual analysis results provided by human experts (pathologists).
  • The DC will develop a Graphical User Interface (GUI) that allows to run the algorithm either in a test environment (demonstrator implementation) and/or the commercial image analysis platforms provided by the hosting institution (TissueGnostics).
  • The DC will document his/her work in a Quality Management and ISO 13485-compliant way (training and instructions to be provided by the hosting institution).

Principal techniques employed in this project: microscopy, image analysis and object segmentation, spectral unmixing, machine & deep learning solutions.

Starting date: 1. October 2024

Principal Investigator / Industrial supervisor: Dr. Rupert Ecker (TissueGnostics GmbH)

Academic supervisor: Assoc.-Prof. Isabella Ellinger (Medical University of Vienna)

The DC will work at TissueGnostics GmbH and be enrolled in the PhD programme of the Medical University of Vienna.

 

Conditions and Remuneration

Extent of employment: Full time

Duration of employment:Limited to 36 months.

The EU has provided the following contributions for the recruited doctoral candidates:

  • Living allowance:       € 43,370.40 per year*
  • Mobility allowance:    € 7,200.00 per year
  • Family allowance:      € 7,920.00 per year, if applicable**

Estimated annual gross salary (not including the employer’s social contributions): € 40,245.32 + family allowance, if applicable.

* = € 40,800 multiplied with the country correction coefficient, to ensure equal treatment and purchasing power parity for all recruited doctoral candidates.

** the family allowance is given only to those with families defined as persons linked to the researcher by (i) marriage, (ii) a relationship with equivalent legal status to a marriage, or (iii) with dependent children.

The Doctoral candidates will be employed with an employment contract. The provided figures are subject to national deductions for social security, income tax, etc.The final salary will be clarified during the interview and confirmed upon appointment.

eRaDicate will cover three years of full-time research. Final contract length and extension options will depend on the host institution and will be clarified during the interviews and confirmed upon appointment.

Requirements

Research Field
Computer science
Education Level
Master Degree or equivalent
Skills/Qualifications

General requirements for admission into eRaDicate

  • Applicants must be eligible (see eligibility criteria below)
  • Applicants must hold a BSc, MSc, or equivalent degree in a related subject area, as required by the specific host organization.
  • Applicants must have the necessary academic skills and background to make the success of a doctoral degree. The skills needed are project-specific.
  • Applicants must be sufficiently proficient in written and spoken English (host organization-specific requirements apply).
  • Applicants must work exclusively and full-time for the PhD research project. The applicants must not have any additional (part-time) jobs.
  • Applicants must fulfil the requirements of the recruiting institutions.

Furthermore, all future DCs of eRaDicate should demonstrate:

  • A high willingness to travel.
  • Independent problem-solving skills.
  • High resilience and flexibility.
  • Excellent communication skills.
  • Integrity, team spirit, dedication to science and learning, dependability, punctuality, pro-activity.
  • Interest in working in an intersectoral, interdisciplinary team and learning new techniques, methods, etc. also outside their comfort zone.
  • A high competence level in scientific writing and public speaking as required by the discipline of the project.
  • Proficiency with computers, office, web-based learning.
  • Willingness to participate in outreach activities, conferences, extracurricular events, etc.
Specific Requirements

Required

  • Master degree in Bioinformatics, Computer Science or a related subject.
  • Experience with biomedical image analysis and data visualization.
  • Knowledge of the programming language Python; optionally also other languages like JULIA or R.
  • Ability and readiness to work on deadlines.
  • Willingness to teach, train, and supervise undergraduate and MSc students.
  • Proficiency in written and spoken English; proof required, German is a plus.
  • The applicant must be eligible to enrol in a PhD programme at the Medical University of Vienna; the Ph.D. programme asks for a minimum proficiency requirement standard of English level B2.

Desired

  • Experience with microscopy and histology.
  • Experience with cancer tissue and studies, esp. ovarian cancer and/or colorectal cancer is a plus.
  • Knowledge of C/C++.
  • Experience with cytometry, spectral unmixing and spatial profiling is a plus.
Languages
ENGLISH
Level
Excellent

Additional Information

Eligibility criteria

The applicant must comply with the following criteria to be eligible for any project in eRaDicate:

  • Applicants must fulfil the mobility rule: Applicants must not have resided or carried out their main activity (work, studies, etc.) in the country of the host organisation for more than 12 months in the 3 years immediately before the recruitment date. (Compulsory national service, short stays such as holidays, and time spent as part of a procedure for obtaining refugee status are not taken into account.) Proof required.
  • Applicants must not hold a PhD or equivalent doctoral degree. (M.D. is eligible)
  • Applicants must not have a conflict of interest with their future supervisors (family, relationship, economic interest…).
Selection process

The eRaDicate selection procedure for DCs will be open, transparent, merit-based and in line with the European Code of Conduct for the Recruitment of Researchers.

The recruitment process consists of an initial written application. Eligible applications will be ranked by a selection committee.

Those not selected will be informed. Shortlisted applicants will be invited for interviews at the selected host institution(s), preferably online, or where possible, in person. A further round of interviews may be required.

Interviewed candidates will be ranked and invited to join eRaDicate in order of their ranking. This process may take a few weeks. We will keep a small number of candidates on a reserve list just in case candidates pull out before the final recruitment stage. Successful candidates will be informed as soon as possible after the interview.

Successful candidates will be subsequently enrolled into the PhD programmes of the respective universities. This is a separate process that may require additional documentation and possibly qualifications like language tests. These will be made known to candidates.

MSCA will cover three years of full-time research, but the final contract length and extension options will depend on the host institution.

eRaDicate pursues a policy of equal opportunities on matters of gender and disability.

Application deadline: 30.4.2024. We may accept applications after this date, until all positions are filled.

Additional comments

Application

https://www.eradicate-project.eu/recruitment/

Applicants are requested to submit their application for one or two positions within eRaDicate electronically (docx of pdf format).

The application should contain (please adhere to the naming conventions for the documents as laid out in the application form):

  • A completed application form (download from https://www.eradicate-project.eu/recruitment/), including an indication of which 1-2 preferred laboratories/research projects within eRaDicate you would like to join
  • Research Exposé: Maximum two pages on your previous research (e.g. BSc or Master’s thesis). The aim is to evaluate your scientific writing skills and ability to present information in a precise and concise way.
  • Current academic CV (max. 4 pages)
  • Graduation certificate/s (if available) and academic transcript incl. university grades. Foreign documents must be sent as certified English translations. These documents must show the grades attained in exam periods, where applicable, and evidence that the required degree will be obtained by the expected time of recruitment if it has not already been awarded.
  • Proof of English language proficiency.
  • Valid ID & proof of eligibility (image of a valid ID, e.g. passport or identity card, AND proof of your employment or studies within the last three years).
  • Two letters of reference in support of your application + filled out referee form. Applicants will be responsible for ensuring that referees submit these letters to coordinator-eradicate@meduniwien.ac.at in time.

All documents must be sent to: coordinator-eradicate@meduniwien.ac.at

Only complete applications sent in will be considered for the selection procedure. The shortlisted candidates at some of the partner institutions might then need to apply also through the institution’s official recruitment channels.

Website for additional job details

Work Location(s)

Number of offers available
1
Company/Institute
TissueGnostics GmbH
Country
Austria
City
Vienna
Postal Code
1020
Street
Taborstraße 10

Contact

City
Vienna
Website
Street
Taborstrasse 10/2
Postal Code
1020