May. 20, 2020

Research Scientist Position
Brain Image Analysis Unit
Center for Brain Science (W20016)


Brain Image Analysis Unit, Integrative Computational Brain Science Collaboration Division, Center for Brain Science (Unit Leader, Dr. Henrik Skibbe)

Research Area

Computational Science, Interdisciplinary


Image Analysis,Deep Learning,Biomedical Image Processing,Artificial Neural Networks, Machine Learning

Research Field

As part of the interdisciplinary Brain/MINDS project (https://brainminds.jp/en/), the Brain Image Analysis Unit develops new techniques to analyze multimodal marmoset brain image data, such as high-resolution two-photon microscopy images, DTI, or resting-state functional MRI.

Machine learning techniques such as deep learning are integrated into new algorithms to improve state-of-the-art processing and analysis of brain imaging data.

Emphasis is placed on developing methods for image registration, image stitching, tracking of neurons and axon fiber bundles, detection, and segmentation of structures and denoising, enhancement, and visualization of images.

https://cbs.riken.jp/en/faculty/bia/  https://bia.riken.jp/

Job title and job description

Job title, available positions

Research Scientist, 1 position

Job description

The selected candidate will join the interdisciplinary Brain/MINDS project, and as a member of the unit will contribute to the development and implementation of image processing and image analysis techniques with a focus on (marmoset) brain image data. The candidate will be responsible for the processing of microscopy images of gene expression patterns in marmoset brain images. This includes the segmentation and 3D reconstruction (stack alignment) of the gene expression signals. Visit our website https://bia.riken.jp/jobs.php.html for further details.


The candidate should have or be expecting to receive a Ph.D., by the time of employment, in related fields and have

  • relevant research skills and experience in developing deep learning techniques for the analysis/processing of images, demonstrated by high-quality publications.
  • expertise in biological/medical/neural image processing, image registration, computer vision, machine learning, optimization, or similar fields, is an advantage.
  • good English communication skills
  • proficiency in a programming language (such as C++/Python/JS)
  • good communication skills and ability to cooperate

Work location

Branch and address

RIKEN Wako (2-1 Hirosawa, Wako, Saitama 351-0198)

Salary and benefits

  1. A one-year fixed-term employment contract to a maximum of the end of the fiscal year 2023(March 31, 2024) with annual evaluation.
  2. RIKEN may adjust the above maximum period of renewability based on a) the employee’s abilities, work load at the time of contract completion, performance and work attitude and b) the continuation of the employee’s center, laboratory or project and RIKEN’s management situation and budget at the time. In principle, employment contracts will not be renewed for individuals older than 65 years.
  3. The employee’s period of fixed-term employment cannot exceed 10 years from the initial date of hire (or 10 years from April 1, 2013 for fixed-term employees already at RIKEN prior to this date). However, employees who have previously worked at RIKEN may be subject to different rules on period of fixed-term employment. Please refer “RIKEN employment duration for fixed-term employees” for more details if necessary.).

In principle, the first two months of employment is considered a trial period.
Salary will be commensurate with qualifications and experience. Commuting and housing allowances will be provided. Social insurance will be applied. Mandatory membership in the RIKEN Mutual Benefit Society (RIKEN Kyosaikai).
This position falls under the specialized duties discretionary work system; one working day will be calculated as 7 hours and 30 minutes.

Days off include public holidays, New Year's holidays (Dec. 29 - Jan 3), and RIKEN Foundation Day.
No smoking on site (designated smoking areas available)
These and other provisions are in accordance with RIKEN regulations.
RIKEN is promoting a Gender Equity Program by taking various measures to create a workplace where both men and women are able to give full rein to their talents and abilities. When applicants are judged to be equally qualified on the basis of fair and impartial criteria, women applicants will be given preference.

Also, eligible for an exemption from repayment for category 1 scholarship loans provided by the Japan Student Services Organization before fiscal year 2003, and eligible applying for the MEXT Grants-in-Aid for Scientific Research (Kakenhi).

Application and required documents

Required documents

  1. Complete CV (with photo and email address)
    (RIKEN CV: WORD(56KB) or EXCEL(159KB) )
    ①(RIKEN CV)*Write the RIKEN job ad number “W20016”, indicated in the parentheses next to the job title, in the RIKEN job ad number section in the upper right corner of your CV.
    ②(Original CV)*Write down in the notes section of your CV the number written next to the title of the job position (e.g. W20016).
  2. Publication list
  3. Research achievements (within 2 pages including figures)
  4. Two of your publications that best represent your expertise or interests (as PDF). It is ok that one of them is a recent, unpublished paper / technical report
  5. Research interests and research proposal (within two pages). Feel free to contact us regarding the proposal
  6. Two letters of recommendation, preferably including one from the current supervisor. If the current supervisor’s recommendation is not available, a recommendation letter from a third party will be accepted.
  7. Consent form for handling personal information based on GDPR
    If you are a resident of the European Economic Area (EEA), you are required to submit the document, “Consent form for handling personal information based on GDPR” with your signature.

    *You will find detailed information about General Data Protection Regulation (GDPR) on the following website:

How to apply

Send the PDF formatted application documents by email attachment to
Dr. Henrik Skibbe, Brain Image Analysis Unit
bia-jobs[at]ml.riken.jp (Replace [at] with @)
The recommendation letters should be sent directly from the recommenders by email attachment to the above email address.
Note: Application documents will not be returned.


Open until the position is filled

Handling personal data

Submitted documents are strictly protected under the RIKEN Privacy Policy and will be used only for the purpose of applicant screening. Personal information will not be disclosed, transferred or loaned to a third party under any circumstances without just cause.

Selection process

Screening with application documents, and then interviews and oral presentations by selected applicants

Start of Employment

August, 2020 (negotiable)

Contact Information / Send application to

Dr. Henrik Skibbe,
RIKEN Center for Brain Science, Brain Image Analysis Unit
2-1 Hirosawa, Wako, Saitama 351-0198
Email: bia-jobs[at]ml.riken.jp (Replace [at] with @)
Please send an email in English.