Job advertisement

Vacancy ID: 286/2022
Closing date: 2022-08-28

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Friedrich Schiller University is a traditional university with a strong research profile rooted in the heart of Germany. As a university covering all disciplines, it offers a wide range of subjects. Its research is focused on the areas Light—Life—Liberty. It is closely networked with non-research institutions, research companies and renowned cultural institutions. With around 18,000 students and more than 8,600 employees, the university plays a major role in shaping Jena’s character as a cosmopolitan and future-oriented city.

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Scientific Researcher
on the iDiv flexpool Project: “Archives4BioDiv
- computer-based methods for
digitizing historic vegetation data and maps”

commencing on 1 November 2022 or at the earliest opportunity limited to 30 September 2024. This is a full-time position with 40 hours per week; place of work is the Institute of Ecology and Evolution of the FSU Jena with joint membership in the working groups “Data-intensive Systems and Visualization” (Patrick Mäder, Jena and Ilmenau) and “Vegetation Ecology” (Markus Bernhardt-Römermann, Jena).

Background:
The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig is a National Research Centre funded by the German Research Foundation (DFG). Its central mission is to promote theory-driven synthesis and data-driven theory in this emerging field. It is jointly hosted by the Martin Luther University Halle-Wittenberg (MLU), the Friedrich Schiller University Jena (FSU), the University of Leipzig (UL), and the Helmholtz Centre for Environmental Research (UFZ). For more information please visit: www.idiv.de.

The project:
In this project, we aim to bring together the ecological research on biodiversity changes and the research on modern computer-based methods focusing on AI-based segmentation and recognition methods.

Repeated observations are key to describe trends of biodiversity change. As most monitoring programs started only recently, they miss retro-perspective long-term developments. Archive data are an option to extend time series to the past.This project (“A Window to the Past – The Use of Archive Data for Collecting Baseline Information on Biodiversity (Archives4BioDiv)”) contributes to the emerging field of bioinformatics and investigates the chances and limitations of modern computer-based techniques for making historic archive data available for biodiversity research. We aim on developing computer-based methods for i) the construction of spatially-explicit time series of forest type development using repeated forest inventory maps from 1850-2000. About 1500 of such maps are available in time steps of up to 20 years; ii) the digitization of historic vegetation records from archives adapting latest AI-based segmentation and recognition methods. Several thousand of historic records from systematic surveys covering 1940 to 1990 are available; iii) the exemplary matching of forest development in time with repeated vegetation surveys to demonstrate the potential of such methods to identify biodiversity changes and drivers.

We are searching for a scientist with a strong expertise in bioinformatics who is interested to foster the development of bioinformatics applications that may help ecologists to digitize huge amounts of archive data and make these available for biodiversity research.

Your responsibilities:

    • Develop and comparatively evaluate segmentation methods to extract region annotations from digitalized maps
    • Develop and comparatively evaluate text recognition (OCR) methods to extract information from digitalized forest inventory records
    • Coordinate research between the research groups in Jena and the data owner (FFK Gotha)
    • Guide the work of technical assistants and student helpers to digitize historical maps and plot records (creation/ enhancement of training data sets)
    • Analyze the acquired data to uncover spatio-temporal changes in forest management and species composition

Your profile:

    • Master’s degree/Diploma in informatics, bioinformatics or a comparable relevant field
    • knowledge and experience in applying machine learning approaches to computer vision problems, ideally for segmentation and text recognition tasks
    • knowledge in the use of geographical information systems (GIS) would be beneficial
    • experience in the use of a machine learning framework and the utilized programming language, e.g., Python and Tensorflow or PyTorch, Matlab, or R
    • knowledge of the German language is advantageous (at least the willingness to learn German)
    • interest in working in an interdisciplinary environment (computer scientists and ecologists)

We offer:

    • Work in a dynamic, international, and interdisciplinary environment in the beautiful city of Jena
    • Opportunities to develop and advance scientific networks
    • Flexible working hours and a family-friendly working environment
    • Participation in our iDiv postdoc career support programme
    • Attractive fringe benefits, e.g. capital formation benefits (VL), Job Ticket (benefits for public transport), and an occupational pension (VBL)
    • Remuneration based on the provisions of the Collective Agreement for the Public Sector of the Federal States (TV-L) at salary scale E13 — depending on the candidate’s personal qualifications — including a special annual payment in accordance with the collective agreement.

Participating Institutions:

All applications should include:
•Cover letter describing the motivation for the project, research interests, and relevant experience
•Complete curriculum vitae including names and contact details of at least two scientific references
•A digital copy of MSc certificate / Diploma

Candidates with severe disabilities will be given preference in the case of equal qualifications and suitability.

iDiv is committed to establishing and maintaining a diverse and inclusive community that collectively supports and implements our mission to do great science. We will welcome, recruit, develop, and advance talented staff from diverse genders and backgrounds.

Queries concerning the application process should be directed to flexpool@idiv.de, for project-related questions, please contact Prof. Patrick Mäder (patrick.maeder@tu-ilmenau.de) or Apl.Prof. Markus Bernhardt-Römermann (markus.bernhardt@uni-jena.de).

Are you eager to work with us? Kindly send your application, quoting the vacancy ID 286/2022, via our application portal at

https://apply.idiv.de

by 28.08.2022.

While we prefer applications via this portal, hard-copy applications may also be sent to:

German Centre for Integrative Biodiversity Research –iDiv (Halle-Jena-Leipzig),
Scientific Networking,
Puschstr. 4,
04103 Leipzig.

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