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Prof. Anna Korzyńska and Prof. Dorota Pijanowska, representing the Laboratory of Processing and Analysis of Microscopic at the Department of Hybrid and Analytical Microbiosystems of the Nalecz Institute of Biocyberntics and Biomedical Engineering Polish Academy of Sciences (Warsaw, Poland) IBBE PAS, are interested in receiving Expressions of Interest of potential candidates for the Marie Sklodowska – Curie Doctorate Network (MSCA-DN-2021) call.

The title of the proposed project: AI based methods of recognition and quantification of breast cancer infiltrating lymphocytes in the tumor microenvironment

The overarching goal of our project is to perform a research on methods supporting the evaluation process of virtual slides breast cancer stained tissue samples to classify the breast cancer subtypes and the probability of relapse for distant metastasis.

For BosomShield, we are looking for a doctorate candidate will have the following responsibilities:
• She/he will perform a research on methods supporting the evaluation process of virtual slides means digital versions of stained tissue preparations in order to propose and verify methods of supporting physicians in their diagnostic, predictive or prognostic work with breast cancer patients.
• She/he will organize the data preparation process and conducting the explainable neural network learning based on the needs reported by coworkers and consultants from Bosom Shield Consortium.
• She/he will design and develop software that performs the inference suited to the need of CAD system which will be an outcome of the project.
• She/he will test using a large set of data, correlation the results of analyzes with the quantities and divisions into classes and categories, as well as therapeutic facts, etc, proposed by physicians.
• She/he will publish the methods and tools for research and the results of applying methods to solve some specific categories of medical problems in journals with IF>1
• She/he will collaborate with diverse teams of scientists and engineers to build an advanced system for BosomShield.
• She/he will design and develop cutting edge methods based on brittle computer vision and machine learning algorithms.
• She/he will help advance R&D by finding problems, implementing elegant solutions, and building tools that enable the team to move forward and to measure progress.

We are looking for talented and innovative self-motivated young scientists, strongly committed to high quality frontier and multi-disciplinary research and able to add new insights to the existing IBBE PAS core expertise.
IBBE PAS as Hosting Institution located at OCHOTA Scientific Campus (Warsaw, Poland), has all the technical and scientific facilities for carry out this project.

Bio of the university and the research group and the benefits of the position:

The Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences (IBBE PAS) was established in 1975. Currently it is the largest center of biomedical engineering in Poland. The Institute has a long history of training of several generations of experts in the biomedical engineering. The IBBE PAS mission is to develop and implement new technologies, devices and supportive theoretical tools for medical diagnosis and treatment aimed at prolonged and improved quality of life of patients with chronic and civilization diseases. The research carried out in the Institute is focused on fusion of engineering and the life sciences that promotes scientific discoveries and the invention of new biomedical technologies.

The Laboratory of Processing and Analysis of Microscopic conducts research in the field of processing and analysis of microscopic images and their sequences created in various types of microscopy. The images document the behavior or condition of medical and biological samples relevant to the medical research and practice. The analysis concerns both the quantitative description of cells and tissues, and their qualitative description - tissue architecture, cell dispersion or aggregation, as well as the description of the behavior and dynamics of cell growth in cell cultures. For quantitative analysis, the methods of object recognition, detection, and segmentation in the classic version, as well as the modern methods based on neural networks, are used. The results of our work support the physicians and biologists in the difficult time-consuming assessment of stained tissue sections or cell smears with automatic or semi-automatic methods of computational pathology.

The candidate will benefit from the participation in project Bosom Shield by obtain high-level training in breast cancer research, in writing scientific papers and gaining skills haw work in large group and synergistically achieving the overall goal of the project. The candidate gains experience in the development of careers underpinned using diverse disciplines, digital radiology, pathology, biomedical, AI, privacy, and software development.

Benefits:
• a full-time position (1.0 FTE) of 6 months with the possibility to prolongs up to 3 years
• a salary of 2000 € gross per month for a full-time job
• a family allowance, if applicable
• benefits from employing offer: e.g. additional health insurance
The successful candidate will first be offered a temporary position of six months with the option of renewal up to three years. Prolongation of the contract is subjected to sufficient progress in the six months.

ELIGIBILITY CRITERIA

At the attempted deadline for the submission of the proposals (30/07/2022):
- Experienced Researchers:
• Scientific achievements in the field of biomedical engineering, computer science, physics, mathematics as well as medicine or biology documented in publications or authorship in software in use.
• At least 1 research project in which the Candidate participated or led will be additional advantage.
• Knowledge of deep learning concepts and experience with deep learning environments (eg.: TensorFlow, PyTorch, etc).
• Excellent practical software engineering ability, particularly Python and C/C++.
• Knowledge of medical image analysis and working with image data.
• Masters degree.
• Collaborative spirit.

- Nationality: Any.

- Mobility: The researcher must not have resided or carried out his/her main activity (work, studies, etc.) in the country of the host organization for more than 12 months in the 3 years immediately prior to the deadline for submission of proposals (a relaxed rule for Career restarting and Reintegration).

- Must be fluent in English (both written and spoken).

SELECTION PROCESS

Researchers willing to apply should check that they fulfil the eligibility criteria and then send an expression of interest, consisting of:
• Scanned copy of identity card, resident's card or passport currently in force.
• Curriculum Vitae (Any research career gaps and/or unconventional paths should be clearly explained so that this can be fairly assessed by the evaluators; if you are a forcibly displaced researcher, please explain your situation in the CV; if you have been residing in Poland in the last 3 years please provide the exact duration and motives of your stay and be prepared to provide the documentation proving it during the redress phase if required by the Project Manager). We recommend you to use the Europass CV template.
• Scanned copy of the certificate of the official academic qualification or proof of payment of the fees for the issuance of the certificate that allows the holder to access the doctoral studies. Students who hold Master degrees should present the scanned copies of their master's degrees.
• Scanned copy of academic transcript of the qualification equivalent to a bachelor's degree.
• Scanned copy of academic transcript of the master's degree.
• Two signed and scanned reference letters.
• A motivation letter, explaining his expertise and how the candidate is suited for the position she/he applies for.
• List of the publication (books, articles in journals, papers published in the materials of scientific conferences) as well as patents, patent applications and major research studies used in clinical practice or references describing role of candidate in developing software system or biomedical tools.
• The copies of two publications of own research in journals
• The list of completed research projects, including the sources of financing and the financial dimensions and scientific cooperation with foreign countries
• the list of national and international scientific societies and committees of which the candidate was or is a member
• the declaration of the candidate that in the event of winning the competition, IBIB PAS will be their primary place of work
• Please add the candidate's declaration of consent to the processing of personal data for the purposes of this competition in the form of: I consent to the processing of my personal data by the Nalecz Institute of Biocybernetics and Biomedical Engineering PAS with headquarters at ul. Księcia Trojdena 4, 02-109 Warsaw, for recruitment purposes. Personal data will be processed on the basis of art. 6 sec. 1 lit. a of the Regulation of the European Parliament and of the Council (EU) 2016/679 of 27 April 2016 on the protection of individuals with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46 / EC (general regulation on data protection Journal of Laws UE.L.2016.119.1 of May 4, 2016). At the same time, I consent to the processing of my personal data for the purpose of future recruitment.

HOW TO APPLY

• Expressions of interest must be submitted to your account through https//:bosomshield.eu.
• Researchers willing must apply to only one positions of the aforementioned 10 positions.
• DCs will be pre-selected on the basis of internal evaluation.
• Candidates will be informed of the results of the pre-selection two weeks/10 days after the deadline.
• Interview between the highest ranked candidates of the pre-selection will be organed by the supervisors to select the final candidate.

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