Seeking a Postdoctoral Researcher (26-823)

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Laboratory

Brain Image Analysis Unit
Integrative Computational Brain Science Collaboration Division
RIKEN Center for Brain Science
(Unit Leader：Henrik Skibbe)

Outline of Laboratory

The Brain Image Analysis Unit develops machine-learning methods, primarily deep learning, to reconstruct the primate brain from large-scale microscopy and MRI data. As part of the Brain/MINDS 2.0 project, we are building a whole-brain, multimodal map of the marmoset, integrating high-resolution two-photon and bright-field microscopy, spatial transcriptomics, anterograde tracing, and diffusion MRI, into a single 3D atlas. This puts us in the unusual position of having both genuinely hard methodological problems (gigavoxel volumes, dense neuron tracing, cross-modal registration) and the rare, large-scale data to work on them, where building usable ground truth is itself a central challenge. We work at the interface of computer science, neuroscience, and medicine, and we build methods to be used, not only published.

Job title and Job description

Job title

Postdoctoral Researcher: 1 position
Postdoctoral Researcher is defined as those with a doctoral degree of 5 years or less.

Job description

For the Brain/MINDS 2.0 project, our unit develops deep-learning methods for large-scale microscopy and MRI analysis of the marmoset brain. Recent publications: Brain Image Analyis Unit

We are seeking candidates to join the Brain/MINDS 2.0 program, passionate about developing deep learning algorithms for microscopy and MRI brain image analysis. Our current focus is on neuron tracing and axon reconstruction, and we welcome strong candidates across the following related areas:

Neuron tracing and axon reconstruction in dense 3D tracer data using (probabilistic) deep learning
Generative models for synthetic ground-truth data for dense 3D neuron tracing
Deep learning for very large 3D images that exceed GPU memory
Cross-modality image registration with deep learning (e.g. microscopy-to-MRI/CT), beyond mutual-information metrics
Foundation models and large language models for biomedical image data
Deep-learning diffusion-MRI tractography validated against same-animal anterograde tracer data

While experience in biomedical image analysis is beneficial, it is not mandatory.

The job description may be changed during the contract period or upon contract renewal to the extent described above.

Qualification

Candidates should hold, or are expected to obtain a Ph.D. degree by the date of employment in a field related to our research focus, such as computer science, biomedical engineering, or a closely related discipline. We expect a demonstrated proficiency in developing deep learning techniques for image analysis/processing, evidenced by publications in reputable peer-reviewed journals or major conferences in relevant fields. Additional expertise in areas like neuron tracing or curve/tree reconstruction, probabilistic modeling and Bayesian inference, diffusion MRI / tractography, biological/medical/neural image processing, image registration, computer vision, machine learning, optimization, and large-scale or out-of-core processing of 3D image data will be considered a significant asset.

A level of English sufficient for academic writing and verbal communication is required. Candidates should also be proficient in programming, preferably with experience in Python or a similar language at an advanced level, ideally including experience with deep-learning frameworks such as PyTorch or TensorFlow. We value the ability to collaborate effectively in a multidisciplinary team, combining strong technical and interpersonal skills.

Work location

RIKEN Wako Campus (2-1 Hirosawa, Wako, Saitama 351-0198)
RIKEN may order the employee to change work locations, if necessary.

Salary and benefits

1.A one-year fixed-term employment contract, renewable based on evaluation, to a maximum of the end of March 31, 2030
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 70 years.

In principle, the first two months of employment are considered a trial period.

Salary will be an annual salary based on experience, ability, and performance, and will consist of a base salary and a variable salary. The variable salary will be determined each fiscal year based on experience, ability, and performance.
Discretionary work, commuting and housing allowances will be provided. Social insurance will be applied.

The approximate amount of salary at the time of employment

The total amount of monthly discretionary work allowance and monthly salary at the time of hiring will be 382,610 JPY or more.

RIKEN has implemented a telecommuting system that allows employees to work from home or other locations permitted by RIKEN.

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.
Paid leave includes annual paid leave (up to 20 days depending on the month of employment), special paid leave (caring for a sick child, family nursing care, etc.), and work life balance holidays (up to 7 days depending on the month of employment).
There are also additional leave systems such as maternity leave, childcare leave, and family nursing care leave.
Smoking is entirely prohibited on site.
These and other provisions are in accordance with RIKEN regulations.
Mandatory membership in the RIKEN Mutual Benefit Society (RIKEN Kyosaikai).

*Eligible to apply for the MEXT Grants-in-Aid for Scientific Research (Kakenhi).

RIKEN is actively undertaking initiatives to promote gender equality and diversity, and moving forward with the establishment of a diverse and vibrant research environment. If multiple candidates are found to have the same aptitude following a fair assessment, active efforts will be made to recruit female candidates.

The Wako Campus has an on-site daycare, RIKEN Kids Wako. For details, please send an email to kids@riken.jp.

Application and required documents

Required documents

1.Complete CV or CV
- *Write the RIKEN job ad number "26-823", 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.List of research achievement and publications
(including ResearcherID or Google Scholar ID, if available)
3.External funding awarded
4.Summary of research experience to date
5.Reason for applying for the post
6.2 letters of recommendation (including one from the current supervisor, If available)
- *Please specify the referee's contact information (Name, affiliation, job title, phone number, and email address)
7.Agreement on handling of personal information (Handling of personal information based on the Hiring Privacy Policy, the General Data Protection Regulation, and the UK General Data Protection Regulation)
Please review the following web page before submitting the consent form.:

How to apply

The above documents, except the letters of recommendation, should be combined into a single ZIP file and uploaded to the following link:
For Postdoctoral Researcher position, Brain Image Analysis Unit, RIKEN Center for Brain Science

The file name of the ZIP should contain your contact email address.
After you upload the ZIP file, please let us (bia-jobs@ml.riken.jp) know the file name of the uploaded file.

Letters of recommendation must be directly submitted from the referees to the following link with the file name " RIKEN Center for Brain Science Postdoctoral Researcher [applicant's name] (Letter of recommendation)". Please specify the applicant's name, and referee's name and contact information in the letter of recommendation

For Postdoctoral Researcher position, Brain Image Analysis Unit, RIKEN Center for Brain Science

After the referees upload the letter of recommendation, please let us (bia-jobs@ml.riken.jp) know the file name of the uploaded file.
If a confirmation email is not received within 7 days after submission, please contact: bia-jobs@ml.riken.jp

Note: All the submitted documents will not be returned.

Deadline

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 at RIKEN. Personal information will not be disclosed, transferred or loaned to a third party under any circumstances without just cause.

Selection process

Application screening and interview for selected applicants

Notification of hiring decision

The notification of hiring decision (conditional offer of employment) regarding this selection shall be carried out through the presentation of an Employment Contract or a Conditional Offer of Employment issued by RIKEN.

Start of Employment

As soon as possible after the candidate is selected

Contact Information

RIKEN Center for Brain Science
Integrative Computational Brain Science Collaboration Division
Brain Image Analysis Unit
Email: bia-jobs@ml.riken.jp
For inquiries, please send an email.