Tag Archives: Career

Python software developer for ilastik

Python software developer for ilastik

Location: Heidelberg, Germany
Staff Category: Staff Member
Contract Duration: 3 years
Grading: 4, 5 or 6, depending on experience and qualifications
Closing Date: 3 June 2018
Reference Number: HD_01306

The European Molecular Biology Laboratory (EMBL) is one of the highest ranked scientific research organisations worldwide. The Headquarters Laboratory is located in Heidelberg (Germany), with additional sites in Barcelona (Spain), Grenoble (France), Hamburg (Germany), Hinxton near Cambridge (UK), Rome (Italy).

EMBL is seeking a highly motivated software developer to join the group of Dr. Anna Kreshuk. The research of the group is concerned with the development of machine learning tools for bioimage analysis. The successful applicant will join the team which develops the ilastik toolkit for interactive learning and segmentation.

Ilastik is a popular open source tool which allows users without image processing expertise to train classifiers interactively, segment images, extract and classify features and track dividing objects.

We are looking for a developer for the following tasks:

  • Improve the integration of ilastik with other popular tools (ImageJ, Knime, CellProfiler, etc)
  • Simplify the development of new workflows and flatten the learning curve for outside contributors
  • Support and expand the user and developer community (together with rest of the team)
  • Further develop the core of ilastik to extend truly interactive processing to larger datasets and more complex workflows
  • Integrate new algorithms developed in the group into ilastik to make them accessible to life scientists

A couple of words about us: ilastik has been developed in the group of Fred Hamprecht at the University of Heidelberg and at the HHMI Janelia Research Campus. Anna Kreshuk has been leading the development in the recent years and, as she is establishing a new research group at EMBL, the ilastik team is moving with her. With the generous support of the DFG (the central research funding organization in Germany), we can now offer a new developer position. Our plans for the coming years include the overall improvement of the program UI, direct integration with other image processing tools and, from the methodological side, integration of deep learning tools in a form accessible to our users.

Qualifications and Experience

We are looking for an experienced Python developer with strong communication skills, preferably with experience in open source or scientific software development.

The requirements are as follows:

  • Degree in Computer Science or a related technical field or equivalent work experience
  • Excellent knowledge of Python, especially its numerical libraries
  • Working knowledge of C++, pybind11 or other tools for Python/C++ bridging
  • Experience with standard development tools: git, conda, cmake, continuous integration tools
  • Fluent English, oral and written

Optional, but desirable:

  • DevOps experience, including cross-platform builds and remote deployment
  • Java knowledge
  • Qt experience

Application Instructions

Please apply online through www.embl.org/jobs

To give us an impression of your code, please supply a link to an open source repository with your contributions. If you haven’t contributed to open source yet, please fix one of the small issues in the ilastik repo www.github.com/ilastik/ilastik and submit your fix as a pull request. The appropriate issues are tagged with “good first issue”.

Additional Information

We offer:

  • Fun work environment in a small team of open source enthusiasts and machine learning experts
  • A broad spectrum of technological challenges: from deep learning to web development
  • Diverse and international environment of the institute

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises from a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, as well as visa and financial support for relocation and installation, including your family.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

https://www.embl.de/jobs/searchjobs/index.php?ref=HD_01306&newlang=1&pos

Director-Bioimage Analysis Center

Director-Bioimage Analysis Center

St. Jude Children’s Research Hospital, Memphis, TN, USA

Job ID 38440

Overview

We’re recruiting a Director for St. Jude Children’s Research Hospital’s BioImage Analysis Center. This critical role requires a strong leader with proven interdisciplinary experience to assemble a team of computational scientists and establish the computational infrastructure to meet institutional needs to analyze and quantitate microscopy imagery at large scales and high throughput.

Responsibilities

St. Jude is a leader in investing in and implementing emerging imaging technologies to support basic scientific and translational research. In this role, you will partner with research programs institution-wide to amplify discoveries made using St. Jude’s unique array of cutting-edge light and electron microscopes resources as well as high-content screening platforms. Other responsibilities include:

  •  Develop workflows for object detection & recognition, segmentation, classification, metric extraction, and statistical analysis of image data produced by research efforts ranging from the individual researcher up to programmatic, large-scale projects.
  • Direct a team in microscopy image data mining and image processing as well as utilizing existing commercial software packages or developing novel algorithms to extract biologically relevant information from data sets produced at SJCRH.

Our highly collaborative, mission-driven environment requires a team-oriented individual with excellent communication skills and the following qualifications:

Minimum Experience

  • Five (5) years of related experience. Experience in computing or statistical data analysis, as well as, programming experience in using Imaris, Amira, ImageJ or Fiji programs and operating within a Linux system is preferred

Minimum Education

  • Ph.D. in Physics, Computer Science, Electrical Engineering, or related field required

 

When you work at St. Jude, you enjoy:

 

Research that translates: Your work at St. Jude directly impacts patient care and advances discoveries that save the lives of children worldwide.

Stability and growth:  Thanks to generous donors and completive grant support, our scientific progress is never halted and you’ll enjoy unmatched resources to do the science you’ve always dreamed of doing.

Award-winning environment:  St Jude is consistently recognized by Fortune magazine as one of the “100 Best Companies to Work For” and has been named of one of Glassdoor’s top 10 “Best Places to Work” in 2018.

Constant learning: From in-depth training to world-class seminars and symposia, you’ll be given constant opportunities to expand your knowledge, learn new skills and grow in your career.

EEO Statement

St. Jude is an Equal Opportunity Employer

No Search Firms:

St. Jude Children’s Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form and/or method without a valid written search agreement in place and approved by HR will result in no fee being paid in the event the candidate is hired by St. Jude.

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HEIBRiDS – a new Data Science Doctoral Program

Welcome to HEIBRiDS – a new Data Science Doctoral Program in Berlin

Established in 2018, HEIBRiDS is a doctoral research school of 6 Helmholtz-Centers (AWI, DESY, DLR, GfZ, HZB and MDC) in and around Berlin in cooperation with the Einstein Center for Digital Future involving the Berlin univerisities Charité, FU, HU, TU, and UdK.

The scientific focus of the HEIBRiDS raises the profile of the important and growing research in data science and trains the next generation of researchers in this field. Graduates benefit from exciting, interdisciplinary projects, joint supervision and mentorship from excellent researchers, affiliation to two centers of teaching and training excellence, extensive research training and professional development program opportunities, and dedicated funding for participation in international conferences and collaborative visits.

Data Science with emphasis on
• Imaging
• Machine Learning
• Modelling
• Novel Hardware Concepts
• Sequencing
• Visualization

HEIBRiDS focuses on data science from medicine and geo-sciences to information technology and engineering and provides an internationally highly recognized and vivid research environment within these research areas combined with the supervision by an interdisciplinary team and a rich lecture program.

For the 2018 intake HEIBRiDS will offer 10-15 PhD positions for outstanding students holding a master’s degree in quantitative sciences or related subjects. The ideal applicant has experience in the general research area of HEIBRiDS and enjoys working in an interdisciplinary environment. All students are required to meet the regular admission requirements of the Berlin universities’ doctoral programs. As HEIBRiDS aims at interdisciplinary research there is no complete list of master’s degrees eligible for the program and the selection process will not solely consider the grades, but the candidates specialist knowledge in the proposed research area.

Duration of support: 3 years with the option of 1 year extension.

Application deadline is Mar 3, 2018.

More information at: https://heibrids.mdc-berlin.de/intern/start_start_for.php

Career consultation: Bioimaging Analysts today!

NEUBIAS, the network of BioImage Analysts funded by COST until 2020, aims to promote the profession of Bioimage Analysts in the Life Science. To this end, the network will devise best-practice guidelines for the career path of these experts, design surveys to scan for existing curricula of BioImage Analysts, and will aim to define a consensus Curriculum in Advanced BioImage Analysis and to create a Job offer repository.

If you are a BioImage Analyst or identify as an important part of your job to be involved in using/developing Image Analysis within Life science, please fill up this questionnaire and help us describing the state of the art of this new profession and identifying the bottlenecks: https://eubias.org/NEUBIAS/careers/

 

Author: Julia Fernandez-Rodriguez, Leader Work Group 7