Ultrasound and Machine Learning for Automated Monitoring of Maturation States in Atlantic Salmon

About the position

Purpose: Provide relevant measures of the state of maturation of Atlantic salmon by means of automatic interpretation of ultrasonic images to improve fish welfare, optimize production, and reduce costs.

Output: The aim of this PhD project is to develop automated methods based on ultrasound and machine learning for determining various important maturation states of Atlantic salmon with the aim of predicting optimal timing of egg stripping for breeding purposes. This can result in a set of methods that can be applied in the daily production for the Atlantic salmon breeding company AquaGen and commercialized in a joint industry project between CIUS partner InPhase Solutions and the non-CIUS partner AquaGen.

Project description: In a recently finalized PhD project between AquaGen and NTNU, several methods using state-of-the art medical ultrasound equipment to monitor maturity of Atlantic salmon have been established. These methods have been implemented and are used in daily operations by AquaGen. The methods currently rely on manually examining single fish in the broodfish production facilities of AquaGen today. This is a cumbersome process, requiring at least 10 people continuously sedating, handling large salmons of 7-13 kg, and manually scanning and analysing data using medical ultrasound systems on a daily basis.

Supervisors:

Main supervisor: Lasse Løvstakken, Professor, NTNU.

Co-supervisors: Marco Voormolen, CTO, InPhase Solutions AS, Ingun Næve, Researcher, AquaGen AS.

Duties of the position

To use these methods more effectively, there is a need for automatization of ultrasound image acquisition and interpretation and further scientific assessment of the methods. In this project, the image interpretation including segmentation of the relevant anatomical structures and features in a single or a series of images, will be addressed by the candidate by applying machine learning to develop automatic models and algorithms to replace manual interpretation. The project will address the following specific applications:

• A method to automatically estimate the gonadosomatic index (GSI; weight of the gonads as percent of body weight)
• A method to automatically predict egg stripping time in female Atlantic salmon by assessing egg development
• A method to automatically estimate fat content in muscle and the viscera

This project builds on the already developed detailed expertise in CIUS on machine learning in echocardiography and aims to translate this to ultrasound examination of salmon for maturation monitoring and egg stripping.

Required selection criteria

The PhD-position's main objective is to qualify for work in research positions. The qualification requirement is that you have completed a master’s degree or second degree (equivalent to 120 credits) with a strong academic background in [subject area] or equivalent education with a grade of B or better in terms of NTNU’s grading scale. If you do not have letter grades from previous studies, you must have an equally good academic foundation. If you are unable to meet these criteria you may be considered only if you can document that you are particularly suitable for education leading to a PhD degree.

The appointment is to be made in accordance with the regulations in force concerning State Employees and Civil Servants and national guidelines for appointment as PhD, post doctor and research assistant.

• A master’s degree or equivalent education with emphasis on theory and methods from acoustics, (bio)physics, mathematics, signal processing, electronics, or computer science, with a weighted-average grade of B or higher, in accordance with NTNU’s grading system
• Good communication skills in both oral and written English
• Good analytical and programming skills

Preferred selection criteria

• Experience within the field of ultrasound in either medicine or industrial applications
• Experience with methods and / or theory for one of the specific projects listed
• Prior written, scientific output with relevance

CIUS aims to be a world-leading centre for research and innovation in next-generation ultrasound technologies. Candidates for this position will be selected in accordance with this aim. For some projects, it is imperative that the candidate has a proven ability to work in an experimental setting and is willing and interested in doing laboratory work.

Personal characteristics

• Good communication abilities
• Besides technical skills, we are looking for a curious, ambitious candidate who is highly self-motivated to do research and contribute to the innovative work carried out in CIUS

In the evaluation of which candidate is best qualified, emphasis will be placed on education, experience and personal suitability.

We offer

• exciting and stimulating tasks in a strong international academic environment
• an open and inclusive work environment with dedicated colleagues
• favourable terms in the Norwegian Public Service Pension Fund
• employee benefits

Salary and conditions

PhD candidates are remunerated in code 1017, and are normally remunerated at gross from NOK 479 600 per annum before tax, depending on qualifications and seniority. From the salary, 2% is deducted as a contribution to the Norwegian Public Service Pension Fund.

The period of employment is 3 years.

Appointment to a PhD position requires that you are admitted to the PhD programme within three months of employment, and that you participate in an organized PhD programme during the employment period.

The engagement is to be made in accordance with the regulations in force concerning State Employees and Civil Servants, and the acts relating to Control of the Export of Strategic Goods, Services and Technology. Candidates who by assessment of the application and attachment are seen to conflict with the criteria in the latter law will be prohibited from recruitment to NTNU. After the appointment you must assume that there may be changes in the area of work.

It is a prerequisite you can be present at and accessible to the institution on a daily basis.

About the application

The application and supporting documentation to be used as the basis for the assessment must be in English.

Publications and other scientific work must follow the application. Please note that applications are only evaluated based on the information available on the application deadline. You should ensure that your application shows clearly how your skills and experience meet the criteria which are set out above. 

Joint works will be considered. If it is difficult to identify your contribution to joint works, you must attach a brief description of your participation.

Candidates from universities outside Norway are requested to send a Diploma Supplement or similar official document, which describes in detail the study and grade system and the rights for further studies associated with the obtained degree: https://europass.cedefop.europa.eu/documents/european-skills-passport/diploma-supplement. Candidates from non-English speaking countries outside the Nordic countries must provide official documentation of their English competence. Approved tests and results are:

• TOEFL: 600 / writing 4.5 (paper-based test), 92 / writing 22 (internet- based test)
• IELTS: 6.5, with no section lower than 5.5 (only Academic IELTS tests accepted)
• Cambridge Certificate in Advanced English (CAE) or
• Cambridge Certificate of Proficiency in English (CPE): grade A or B

General information

A good work environment is characterized by diversity. We encourage qualified candidates to apply, regardless of their gender, functional capacity or cultural background. 

NTNU is committed to following evaluation criteria for research quality according to The San Francisco Declaration on Research Assessment - DORA.

As an employee at NTNU, you must at all times adhere to the changes that the development in the subject entails and the organizational changes that are adopted.

Information Act (Offentleglova), your name, age, position and municipality may be made public even if you have requested not to have your name entered on the list of applicants.

For further information about the positions, please contact either:

Industry liason and researcher, Svein-Erik Måsøy, telephone: +47 92625082 or email: svein-erik.masoy@ntnu.no.

Professor, Lasse Løvstakken, telephone: +47 91347206 or email: lasse.lovstakken@ntnu.no.

For information concerning the application process, please contact: HR Consultant Julie Hoff, telephone: + 47 72576984, email: julie.hoff@ntnu.no

The application is to be accompanied by a cover letter explaining how your background and education fit the goals and requirements of the selected project(s) from the list of available positions. Please submit your application electronically via jobbnorge.no with your  cover letter, CV, diplomas and certificates.

Applications submitted elsewhere will not be considered. Diploma Supplement is required to attach for European Master Diplomas outside Norway. Chinese applicants are required to provide confirmation of Master Diploma from China Credentials Verification (CHSI).

If you are invited for interview you must include certified copies of transcripts and reference letters.

Application deadline: 31.07.2020

NTNU - knowledge for a better world

The Norwegian University of Science and Technology (NTNU) creates knowledge for a better world and solutions that can change everyday life.

The Department of Circulation and Imaging (ISB) has 260 employees, and its research units are at the Cardiothoracic Centre at St. Olav’s Hospital, integrated with collaborating clinical divisions. The Department of Circulation and Medical Imaging (ISB) includes anaesthesiology, radiology, radiography, ultrasound, magnetic resonance imaging, exercise physiology, cardiovascular physiology, pulmonary physiology, pulmonary medicine, cardiology, vascular surgery, thoracic surgery and biomedical engineering. The department is also responsible for the Centre for Innovative Ultrasound Solutions (CIUS), the Medical Simulation Centre and the MR Centre. More information about the department is available at http://www.ntnu.edu/isb

Deadline 31st July 2020
Employer NTNU - Norwegian University of Science and Technology
Municipality Trondheim
Scope Fulltime
Duration Fixed Term
Place of service Øya