Category Archives: Jobs

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

IMAGE PROCESSING LAB MANAGER – IT PROJECT MANAGER

IMAGE PROCESSING LAB MANAGER – IT PROJECT MANAGER

Center for Microscopy and Molecular Imaging (CMMI), Biopark Charleroi Brussels South, Belgium

Master of engineering, master in computer science with experience (or a PhD degree) related to image processing.

Applications are invited for a lab manager position to work at the Center for Microscopy and Molecular Imaging (CMMI) in Biopark Charleroi Brussels South, Belgium. CMMI provides the scientific community (universities and private companies) with an integrated and efficient preclinical imaging platform. You will have close interaction with the multidisciplinary team of the center. You will have access to the state of the art pre-clinical imaging systems. You will be responsible for the image data management and original image analysis developments for the facility.

Current imaging modalities at the CMMI:
– Electron microscopy
– Brightfield, fluorescence, confocal microscopy
– Holography microscopy
– High-content microscopy analysis system
– Whole Slide Imaging (digital pathology)
– High-resolution autoradiography
– Magnetic resonance imaging (preclinical)
– PET and SPECT (pre-clinical)
– CT (pre-clinical)

QUALIFICATIONS/EXPERIENCE

● be an experienced engineer or computer scientist ideally with research experience
● have experience in image processing, ideally in biomedical imaging;
● have good programming skills and good notions of software project management
● possess a proven track record in managing and delivering research projects or project management
● have a problem solving oriented mind and a good team spirit, the position involves daily collaboration with the other CMMI members
● ideally possess a track record in securing research funding … DUTIES The candidate will actively participate in the following activities:
● manage contact with internal and external scientific and industrial clients
● design and implement an image repository framework for the CMMI (by looking for existing available solutions)
● implement good software practices for the long term support of image processing and analysis routines
● set up new image processing developments in collaboration with the other members of the center
● disseminate results by actively initiate and participate to scientific publications
● apply to research project calls (regional and international)

LANGUAGE SKILLS

– ENGLISH Good
– FRENCH Good

The position is for four years and it is renewable subject to funding availability.

Contact person: Olivier Debeir odebeir@ulb.ac.be

Scientific Software Developers/Programmers and DevOps Engineer

Scientific Software Developers/Programmers and DevOps Engineer

Max-Planck Institute for Cell Biology and Genetics in Dresden and the Center for Systems Biology Dresden, Germany

https://www.mpi-cbg.de/education-careers/jobs/article/news/scientific-software-developersprogrammers-and-devops-engineer-mf/

 

We have two open positions for

Scientific Software Developers/Programmers and DevOps Engineer (m/f)

to add to our creative and interdisciplinary research team at the Max-Planck Institute for Cell Biology and Genetics in Dresden and the Center for Systems Biology Dresden. We, namely the research groups of Pavel Tomancak and Florian Jug, develop methods and algorithms for image-based systems biology by applying and further developing cutting edge approaches that make use of various computer vision and machine learning techniques. Our work also includes the development of convenient and reusable algorithmic modules and user interfaces that are capable of dealing with gigabytes and terabytes of image data. Our efforts are all funneling into the open community projects Fiji, ImageJ2, and KNIME.

We expect you to become an important and influential figure in our vibrant user and developer community which operates in multiple hot-spots all around the world. Therefore we seek an open-minded and motivated personality to help us further our soft-ware and tool landscape for bio-image analysis, effectively putting needed algorithmic solutions at the fingertips of thousands of academic users world wide. This task naturally comes with the opportunity to visit other members of our community around the world and will bring you in touch with the latest microscopy, VR, and software technology.

In the past years, Dresden has developed into one of the leading scientific centers at a tremendous pace. As a city of about half a million inhabitants, it hosts 19 world-class scientific institutions with a very international community. Dresden was awarded the title City of Science in 2006. It is picturesquely located on the river Elbe, about 2 hour away from Berlin and Prague, and offers a high, family-friendly quality of life at low price level.

Prerequisites
Applicants are expected to have an M.Sc. degree or PhD in Computer Science, Scientific Computing, Software Engineering, Physics, or related areas. Excellent programming skills are required. Most of our codes are written in Java, but we also develop in Python and C/C++. Experience with CUDA and/or OpenCL is helpful. Proficiency with developer tools such as git, Github, Jenkins or Travis, automated test suits, etc. is an essential necessity. An additional requirement is your interest in helping us improve the tool-support for our developer base world wide, making your DevOps experience a certain plus.

Application and Contact
The position is initially limited to 3 years. Salary and social benefits will be in accordance with the regulations of the German TVöD Bund (salary agreement for public service employees) up to EG 13.
We especially encourage women to apply.

The Max Planck Society is committed to employ more people with disabilities and actively seek their applications.

Please submit your complete application in English including a motivation letter, CV, and at least two recommendation letters by April 22nd, 2018 via our online application system (Code: 2018-SSD-2210) at https://recruitingapp-2443.umantis.com/Vacancies/401/Application/CheckLogin/2?lang=eng

If you are currently involved in open-source projects, please provide links to your work.

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden, Germany
www.mpi-cbg.de

 

ZURICH IMAGE AND DATA ANALYSIS SCHOOL 2018

ZURICH IMAGE AND DATA ANALYSIS SCHOOL 2018

Are you a life-scientist needing to quantify microscopy images?

Do you want to learn how to automatically detect objects in images, track spots and cells, build reproducible image processing workflows, deconvolve and enhance microscopy images, and handle massive data? If yes, this school is for you!

What you will learn!

In this one-week school you will get a hands-on introduction to Image Processing and Analysis, with an emphasis on biologically relevant examples. You will learn the fundamentals of image analysis, including macro programming in ImageJ/Fiji, scripting in MATLAB, as well as other software solutions and a range of focused topics.

In the first part of the week, we will cover the process of image formation as it pertains to image analysis: Resolution, correct exposure, point-spread functions, detector noise, Shannon’s sampling theorem, and aliasing. All with a clear focus on application in the lab.

In the second part of the week we will cover a number of focused topics, building on what was learnt during the first days:

  • Call4Help session
  • Scripting in MATLAB
  • Tracking particles and cells in time-lapse recordings
  • Segmentation and classification via supervised Machine Learning in ilastik
  • De-convolution of microscopy images
  • Stitching and registration of stacks of large image data
  • Working on your own project / data

Time: 19th – 24th June 2018

Place: ETH, Zurich, Switzerland

Participation fee: 500 CHF (academia) / 1000 CHF (industry)

For further information please visit this webpage: http://2018.zidas.org/

Szymon Stoma, Beat Schuler & Simon F. Nørrelykke

Image and Data Analysis (IDA) group, Scientific Center for Optical and Electron Microscopy (ScopeM) | EXCITE @ ETH Zurich

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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Image Analysis Expert for Microscopy

Image Analysis Expert for Microscopy

Together with the Scientific IT Support (scits.unibe.ch) of the Faculty of Science, the
Microscopy Imaging Center (mic.unibe.ch) of the University of Bern opens a
position for an

Image Analysis Expert for Microscopy (80-100%)

Tasks

  • Optimise and deploy image and data analysis pipelines for current and new instruments at the Microscopy Imaging Center (MIC)
  • Support MIC users with image processing and analysis challenges
  • Support design of IT infrastructure (hardware and software) for new MIC instruments
  • Organise and implement MIC trainings on image processing, IT infrastructure usage and application software
  • Participate in MIC related research and development projects
Qualifications

  • PhD or equivalent in relevant discipline (bioinformatics, bioimaging, biomedical engineering, computer science, physics, applied mathematics biology etc)
  • Recognised experience in applying and/or developing image analysis tools with Fiji/ImageJ, Icy, Imaris, CellProfiler, MATLAB, Java or Python
  • Outstanding programming and data analysis skills (Python/R, C/C++, GPGPU, deep neural networks)
  • Microscopy/bioimaging experience and familiarity with biological data is an asset, interest in this field is pre-requisite
  • Experience with real-time systems and system administration is an asset
  • Strong team player with service-oriented work style and excellent English communication skills (German is an asset)
Conditions

  • Salary according to qualifications and cantonal regulations
  • Begin 2018-05-01 or by agreement
  • Two years with possible extension

The Microscopy Imaging Center at the University of Bern (MIC) is the interdepartmental platform for high-end microscopy. MIC provides access to state-ofthe-art imaging techniques for researchers from 12 institutes of 3 departments of the University of Bern as well as for external visitors. It collaborates closely with the Science IT Support (ScITS) unit from the Faculty of Science. The successful candidate will be embedded in the ScITS team which maintains university-wide, national and international knowledge networks and is associated with the Mathematical Institute. The ScITS working atmosphere is academic, responsive and cooperative. The office location is next to the Bern central railway station. The successful candidate will be member of the MIC commission. Questions regarding the position can be directed to the ScITS coordinator Dr. Sigve Haug or the MIC coordinator Dr. Ruth Lyck (sigve.haug@math.unibe.ch, ruth.lyck@tki.unibe.ch). Women are encouraged to apply.

Please send your full application with transcripts of diplomas, CV, two references, relevant publications and motivation letter as a single PDF to sigve.haug@math.unibe.ch until March 26, 2018.

Universität Bern, Mathematisches Institut, Sidlerstrasse 5, 3012 Bern
sigve.haug@math.unibe.ch, www.unibe.ch

https://firmenwhitelabel.publisherconnect.ch/firmenwhitelabel/addetail/job/index.htm?adId=10386106&locale=en

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

Senior microscopy expert

Senior microscopy expert

The (Bio-)Imaging Facility of the IST Austria provides state-of the art fluorescence microscopy services, FACS services, as well as custom image analysis and optical development services. We are enlarging our team and are searching for a full time (senior) microscopy expert (f/m).
Are you interested in how your future working place may look like? This video* provides a bird’s eye view of IST Austria.

Responsibilities

  • Support and development of advanced quantitative microscopy-based measurement methods (FLIM, FRAP, TIRF, laser ablation, multiphoton -and atomic force microscopy)
  • Support of basic facility operation: routine care of the microscopy equipment and basic training of the users of the (bio-)imaging facility
  • Operation and support of Fluorescence Assisted Cell Sorting (FACS)
  • Expert advice to users
  • Optionally, support of image analysis projects
  • Optionally, participation in the research projects initiated by research groups

Requirements

  • PhD or relevant education and research experience involving microscopy
  • Proven experience with at least some of imaging approaches: confocal, multiphoton, spinning disc, light sheet, TIRF microscopy is required – AFM, FACS, and/or FLIM/FRET experience will be advantageous
  • Good communication skills in English is mandatory
  • Organizational and project management skills are advantageous
  • Work experience in a core facility and/or academic environment is advantageous

Please find all information about the vacant postion here:
http://ist.ac.at/fileadmin/user_upload/pdfs/Recruiting_documents/2018_01_Job_Ad_MicroscopyExpert_Englisch.pdf

Additional information:
information about IST Austria: https://ist.ac.at/
Scientific service units @ IST Austria: http://ist.ac.at/ssus
The BioImaging Facility @ IST Austria: http://ist.ac.at/ssus/list-of- facilities/bioimaging- facility/

Application:
To apply for this position send your application until March 1st, 2018 in one combined pdf (including CV, certificates and references) by e-mail to: gabriele.buchner-kranzl@ist.ac.at

* In case the ink to the video does not work: https://www.youtube.com/watch? v=nVsWLgkx9uE

Bioinformatician with focus on research support in image analysis

Bioinformatician with focus on research support in image analysis

KTH Royal Institute of Technology, School of Computer Science and Communication

KTH Royal Institute of Technology in Stockholm has grown to become one of Europe’s leading technical and engineering universities, as well as a key centre of intellectual talent and innovation. We are Sweden’s largest technical research and learning institution and home to students, researchers and faculty from around the world. Our research and education covers a wide area including natural sciences and all branches of engineering, as well as in architecture, industrial management, urban planning, history and philosophy.

Department information

The position will be formally placed with the department for Computational Science and Technology (CST) at KTH, but work will be carried out at the Science for Life Laboratory. The CST department conducts research to understand and model physical and biological systems using computational techniques, which require efficient, high performance algorithms and implementations together with advanced visual analysis capabilities. For more information go to https://www.kth.se/en/csc/forskning/cst. The Science for Life Laboratory (SciLifeLab) is a collaboration between four universities in Stockholm and Uppsala: Karolinska Institutet, KTH, Stockholm University and Uppsala University. It combines advanced technology with broad knowledge in translational medicine and molecular life sciences. Since 2013, SciLifeLab has a mission from the Swedish government to run infrastructure to support researchers nationally and to be an internationally leading center for large-scale analyses in molecular life sciences targeting research in health and environment. For more information, visit https://www.scilifelab.se/.

Job description

We are looking for a PhD with a keen interest in implementation and adaption of image analysis algorithms for quantitative analysis of microscopy data to join the SciLifeLab BIIF (https://www.scilifelab.se/facilities/bioimage-informatics/). You will work in short and long-term projects, providing research support and education in image analysis. The BIIF has nodes in both Uppsala and Stockholm, but the assignment includes services to researchers at other universities in Sweden as well. The job includes involvement and organization of courses and workshops in digital image processing and analysis with life science applications. Supervision of master thesis students is part of the assignment. 20% time will be spent supporting projects at the LCI facility in Huddinge.

Qualifications

A PhD in computer vision/image processing (or equivalent), or a PhD in bio-medicine/biology (or equivalent), combined with documented experience of computer programming and development of digital image analysis solutions is required. In addition, the following qualifications are considered highly desireable:

  • Experience with analysis software such as Imaris, ImageJ/Fiji, CellProfiler, NIS and Amira
  • Experience with algorithm development and development of analysis pipelines aiming to quantify and classify biological parameters extracted from microscopy data of e.g. cells and microorganisms in cultures and tissue samples
  • Experience in medical image analysis
  • Experience with teaching and student supervision
  • Proficiency with a scientific programming language (Python, R, or Matlab)
  • Excellent English communication skills, both spoken and written, as well as excellent interpersonal skills Other meriting experiences and skills
  • Postdoctoral experience in image analysis, within or outside academia, especially focused on methods development

Familiarity with deep learning frameworks like Keras, TensforFlow, or PyTorch

Trade union representatives

You will find contact information to trade union representatives at KTH:s webbpage.

Application

Log into KTH’s recruitment system in order to apply to this position. You are the main responsible to ensure that your application is complete according to the ad. Your complete application must be received at KTH no later than the last day of application.

Applications shall include the following documents:
1. Statement of interest including a brief description of experience in bioimage analysis 2. Curriculum vitae
3. Reference contact information
4. Representative publications (or other example of scientific writing)

Please observe that all material needs to be in English.

Others

We firmly decline all contact with staffing and recruitment agencies and job ad salespersons.
Type of employment: Temporary position longer than 6 months
Contract type: Full time
First day of employment: According to agreement
Salary: Monthly salary
Number of positions: 1
Working hours: 100%
City: Stockholm
County: Stockholms län
Country: Sweden
Reference number: D-2017-0987

Contact
Kevin Smith / Assistant Professor, ksmith@kth.se
Maria Engman / HR-administratör, maengm@kth.se

Published  18.Jan.2018
Last application date:  28.Feb.2018 11:59 PM CET

BIO-IMAGE ANALYST RESEARCHER

BioImage Analyst for scientific imaging platform

IBMC/i3S, Porto, Portugal

 

The IBMC – Instituto de Biologia Molecular e Celular is opening of an international selection tender for 1 vacancy of doctorate to perform duties of scientific research in the scientific area of Bio-Imaging, under a work contract with non-fixed term, in order to develop research activities on bio-image analysis at the i3S Advanced Light Microscopy scientific platform . The researcher should collaborate with the platform’s users by providing training and support to solve their problems of image analysis. Additionally, should collaborate in the organization of postgraduate courses in the area. Other functions may include mentoring master and doctoral students.

 

Admission requirements are:

General:

PhD Degree in engineering, mathematics, computer science, physics, biosciences or similar.

Specific:

– experience in digital image processing, analysis and quantification;

– experience with scientific image analysis open source software packages including ImageJ / Fiji;

– experience with programming languages: Matlab, Python, R or Java;

– experience in the design, construction and implementation of workflows for image analysis;

– knowledge of statistical analysis

– previous experience with biological or medical imaging is desirable.

 

 

More informations at: https://www.ibmc.up.pt/sites/default/files/bioimage_analyst_roteiro_paula_sampaio.pdf

 

For informal inquiries, please contact:

sampaio@ibmc.up.pt

 

Candidates shall submit their application from the 15th January 2018 to 10th February 2018 to: http://www.ibmc.up.pt/gestaocandidaturas/index.php?codigo=ROTEIRO1802