Job:Postdoctoral Fellow in High-throughput Imaging
Entering edit mode
2.5 years ago
Recruit ▴ 230

The Opportunity:

We are looking to appoint a highly motivated postdoctoral fellow in high-throughput imaging and image data analysis to join Omer Bayraktar’s group at the Wellcome Sanger Institute.

Our group seeks to explore the vast cellular diversity of cell types in the human body, with a primary focus in the brain. We can now discover cell types across human organs using single-cell genomics. However, our ability to study human cell types in situ within the intact spatial context of tissues is still limited. To create single-cell level 3D maps of human organs, our group will establish large-scale and highly-multiplexed spatial transcriptomics methods. We will further use spatial transcriptomics to discover human disease phenotypes in situ. Our work will ultimately contribute to the generation of a comprehensive single cell level atlas of the human body in health and disease.

About the Project/Team:

You will be joining a new collaborative project as part of the Human Cell Atlas (HCA) at Sanger that aims to develop spatial transcriptomics and tissue imaging at large scale. You will be expected to contribute to the image acquisition software, cyclic RNA and protein labeling of human tissues and image data analysis. You will work closely with a growing team of core scientists and researchers on the pipelining and image data analysis. You will also collaborate with external groups to obtain training in cutting-edge spatial transcriptomics methodology.

The Role:

You will lead an exciting research project in developing high-throughput imaging platforms for human tissue spatial transcriptomics. Your primary objectives will be 1) to create software pipelines for automated microscopy instrument control and cyclic imaging and 2) to create an image analysis workflow for single cell level quantification of image data from human tissues.

Your work will help shape the future research questions and methodology in the lab and you will be supported to develop your own research projects within the scope of the group’s interests. Our exposure to HCA projects at Sanger will also allow you to contribute to tissue applications outside the nervous system. You will be encouraged to participate in the design and planning of these projects.

Essential Skills:

  • PhD in relevant wet-lab subject (e.g. Biology, Physics)

  • Strong background in light microscopy and high-throughput imaging

  • Experience with open source microscopy-control and image analysis pipelines, such as Micromanager, Fiji/ImageJ and scikit.

  • Experience in image data analysis, especially cell segmentation

  • Excellent communication skills

  • Understanding of ethics of working with human tissue samples

  • Experimental troubleshooting skills

  • Excellent planning skills

  • Ability to develop strong collaborative working relationships with diverse team members/stakeholders

Ideal Skills:

  • Experience image database and rendering solutions like OMERO and IDR

  • Experience in building and maintaining bespoke microscopy instrumentation

  • Experience with highly-multiplexed RNA hybridization or sequencing

Other information:

Closing date: 11/12/2019

About Us:

The Wellcome Sanger Institute is a world leading genomics research centre. We undertake large-scale research that forms the foundations of knowledge in biology and medicine. Our findings are used to improve health and to understand life on Earth. Find out more at or follow us on Twitter, Facebook, LinkedIn, Youtube and on our Blog.

Our campus:

Set across 130 acres, just outside of Cambridge, The Sanger Institute is located on the stunning Wellcome Genome Campus. Home to some of the world's foremost institutes and organisations in genomics and computational biology, committed to delivering life-changing science with the reach, scale, and creativity to solve some of humanity's greatest challenges.

Our benefits:

There’s an attractive benefits package on offer at the Genome Wellcome Campus. We appreciate the importance of achieving work-life balance and support this with a number of family and carer-friendly policies. Plus a flexible working policy for those who may wish to amend their working pattern or arrangement. As well as the usual benefits you would expect, we go much further:

25 days annual leave (extra 1 day to a maximum of 30 days for every year you work) Auto-enrolment into a generous Group Defined Contribution Pension Scheme, with enhanced company contribution (for more information, see our Pensions page) Up to 2 days annual paid volunteering leave Up to 10 days paid Emergency Carers Leave per year Family friendly environment including options for flexible and part-time working, an on-site Workplace Nursery salary Sacrifice Schemes for pre-school children and Summer holiday club Life Assurance Cover and a Group Income Protection Scheme (if on a contract of 12 months or more) Enhanced maternity leave and parental leave Access to substantial number of courses and training events onsite Private Healthcare Scheme (after 6 months service) Eyecare and Dental payment plans Concessions and discounts from our corporate perks site

Being part of the Genome Wellcome Campus you will be part of the beautiful working environment with an impressive range of benefits, services and facilities also including:

Free bus service to and from Campus, covering various routes around Cambridge, Saffron Walden and surrounding villages A car-share initiative Free parking A number of on-site venues where you can meet, eat and socialise with colleagues A thriving Sports and Social Club which provides members with subsidised access to a gym, tennis courts, sports hall, fitness classes and a vibrant social calendar of events Find out more about our Genome Wellcome Campus.

We hold an Athena SWAN Bronze Award and will consider all individuals without discrimination and are committed to creating an inclusive environment for all employees, where everyone can thrive.

To apply, please visit:

Omero IDR Scikit Imagej Job • 536 views

Login before adding your answer.

Traffic: 552 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6