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3rd APPN Meeting presentations published!
by Jez,Jakub 12 Jul '19

12 Jul '19

Dear all, We have just published all presentations of the 3rd Meeting and an image gallery! Visit our homepage for download and enjoy the read: https://www.appn.at/3rdappn/ Best regards, Jakub [VBC Logo] Jakub Jez Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77090<tel:+43%20664%208084%2077090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at> Chair, Austrian Plant Phenotyping Network (APPN<https://www.appn.at/>) and Support Group Member of ESFRI EMPHASIS<https://emphasis.plant-phenotyping.eu/> project Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> LinkedIn: www.linkedin.com/in/jezjakub<http://www.linkedin.com/in/jezjakub> [signature_1620261999] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

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Hydroponics+Arabidopis=Araponics
by Jez,Jakub 12 Jul '19

12 Jul '19

Dear all, We are currently running an external hydroponics-based phenotyping experiment in phytotron #1. In case you are interested in hydroponics please feel free to take a look through the window and/or talk to Anneliese. Protocols are also available at our facility. Basically, plants are germinating on agar in a sample holder until the roots reach the fluid medium. Advantages are a highly homogenous and controlled root environment; the possibility of working with different chemicals (fertilizers, hormones, salt, etc.) and the root system is easily accessible for sampling or shovelomics (until a certain developmental stage; then roots get knotted). And: no black flies, so far. Disadvantages: handling and potential contaminations of the agar in the sample holder. The system we use is called Araponics: http://www.araponics.com/ Best, Jakub [VBC Logo] Jakub Jez Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77090<tel:+43%20664%208084%2077090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at> Chair, Austrian Plant Phenotyping Network (APPN<https://www.appn.at/>) and Support Group Member of ESFRI EMPHASIS<https://emphasis.plant-phenotyping.eu/> project Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> LinkedIn: www.linkedin.com/in/jezjakub<http://www.linkedin.com/in/jezjakub> [signature_656262654] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

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PHENOBox upgrade to 12x12 agar-plates (screening of seedlings and roots)
by Jez,Jakub 04 Jul '19

04 Jul '19

Dear all, Together with Natalie, Philipp and Stephan, our summer students, we are currently implementing and upgrading two PHENOBox systems at both locations of the PlantS facility (GMI and MFPL): https://twitter.com/VBCF_PlantS/status/1146382324604526592 The PHENOBox is a semi-automated imaging cabinet for low-throughput RGB phenotyping of tall plants (up to 50cm incl. pot) and was published last year (Djamei group): https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15129 Now, we are upgrading this system by a sample holder for 12x12cm agar-plates for screening of seedlings and for root phenotyping. Also, subsequent image analysis pipelines will be established. On the top to our samples, we would very much appreciate receiving yours (tall plants, agar-plates with seedlings or roots) in order to have a broad range of different samples for establishing robust image analysis pipelines (please don’t let me dick in the facility waste bins for that ;-). We will also design and build templates for standardized positioning of seeds (seedlings and root phenotyping). Your input (your templates) and experienced is appreciated! If you are interested in this project, please feel free to drop by our office for a chat and a look at the PHENOBox. Thanks! Kind regards, Jakub [VBC Logo] Jakub Jez Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77090<tel:+43%20664%208084%2077090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at> Chair, Austrian Plant Phenotyping Network (APPN<https://www.appn.at/>) and Support Group Member of ESFRI EMPHASIS<https://emphasis.plant-phenotyping.eu/> project Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> LinkedIn: www.linkedin.com/in/jezjakub<http://www.linkedin.com/in/jezjakub> [signature_613215582] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

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Program 3rd APPN Meeting published!
by Jez,Jakub 30 May '19

30 May '19

Dear friends, We have just published the program for the 3rd APPN meeting! https://www.appn.at/3rdappn/ Registration still open till the 7th June. Looking forward to meeting you! Best regards from Vienna, Jakub [VBC Logo] Jakub Jez Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77090<tel:+43%20664%208084%2077090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at> Chair, Austrian Plant Phenotyping Network (APPN<https://www.appn.at/>) and Support Group Member of ESFRI EMPHASIS<https://emphasis.plant-phenotyping.eu/> project Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> LinkedIn: www.linkedin.com/in/jezjakub<http://www.linkedin.com/in/jezjakub>

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3rd APPN meeting - Field Phenotyping and Remote Sensing, 13th June, BOKU, Vienna, AT
by Jez,Jakub 09 May '19

09 May '19

Dear friends, The abstract submission deadline for the 3rd APPN Meeting at the BOKU is approaching! If you want to learn about drones and satellites in agriculture, hyperspectral imaging, LiDAR, machine- and deep learning in plant sciences register here: (Free) registration: https://www.appn.at/3rdappn/ Confirmed speaker: Opening speech: Christian Obinger, Vice Rector for Research, University of Natural Resources and Life Sciences (BOKU) Hermann Bürstmayr, Head Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences (BOKU) “Future challenges for Austrian plant breeding and opportunities from modern phenotyping approaches” Clement Atzberger, Head of Institute for Surveying, Remote Sensing and Land Information, University of Natural Resources and Life Sciences and GreenSense GmbH, AT “Determining crop traits through multi-spectral data” Ethan Stewart, Gore Lab, Dep. of Plant Breeding and Genetics, Cornell University, US “The application of a deep learning approach for quantitative disease phenotyping in UAV images” Helge Aasen, ETH Zürich, Dep. of Environmental System Science, CH “Low-altitude / high-resolution remote sensing for field-phenotyping” Ittai Herrmann, The Hebrew University of Jerusalem, R.H. Smith Faculty of Agriculture, Food and Environment, IL “Field crops phenotyping (disease, water status and yield) by spectral remote and proximal sensing” Jan F Humplík, Spichal Lab, Palacky University Olomouc, CZ “Field plant phenotyping using UAV LiDAR system: current state and first experiences.” Pieter Clauw, Nordborg Lab, Gregor Mendel Institute of Molecular Plant Biology (GMI), AT “Combining growth chamber simulations and field experiments to tackle temperature adaptation in Arabidopsis thaliana” Looking forward to meeting you. Best wishes, Jakub [VBC Logo] Jakub Jez Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77090<tel:+43%20664%208084%2077090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at> Chair, Austrian Plant Phenotyping Network (APPN<https://www.appn.at/>) and Support Group Member of ESFRI EMPHASIS<https://emphasis.plant-phenotyping.eu/> project Twitter: @VBCF_PlantS<https://twitter.com/VBCF_PlantS> LinkedIn: www.linkedin.com/in/jezjakub<http://www.linkedin.com/in/jezjakub> From: Jakub Jez <jakub.jez(a)vbcf.ac.at> Date: Monday, March 25, 2019 at 11:52 AM To: APPN community <appn(a)lists.vbcf.ac.at> Subject: 3rd APPN meeting - Field Phenotyping and Remote Sensing, 13th June, BOKU, Vienna, AT Dear friends, It is our pleasure to invite you to the 3rd Austrian Plant Phenotyping Network (APPN) Conference featuring “Field Phenotyping and Remote Sensing”. Last year we put emphasis on root phenotyping (https://www.appn.at/2ndappn_eppn2020-2/) this year the main focus will be (although not exclusively) on field phenotyping and “big” data. Other plant phenotyping topics (controlled environments, root phenotyping and others) will be covered by the respective sessions based on the received abstracts. The meeting will take place on June 13, 2019 at the University of Natural Resources and Life Sciences (BOKU), Vienna, AT. (Free) registration open: https://www.appn.at/3rdappn/ Please feel free to share & spread the word! Looking very much forward to meeting you, Gernot Bodner, Boris Rewald (local organizers) & Jakub Jez

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3rd APPN meeting - Field Phenotyping and Remote Sensing, 13th June, BOKU, Vienna, AT
by Jez,Jakub 25 Mar '19

25 Mar '19

Dear friends, It is our pleasure to invite you to the 3rd Austrian Plant Phenotyping Network (APPN) Conference featuring “Field Phenotyping and Remote Sensing”. Last year we put emphasis on root phenotyping (https://www.appn.at/2ndappn_eppn2020-2/) this year the main focus will be (although not exclusively) on field phenotyping and “big” data. Other plant phenotyping topics (controlled environments, root phenotyping and others) will be covered by the respective sessions based on the received abstracts. The meeting will take place on June 13, 2019 at the University of Natural Resources and Life Sciences (BOKU), Vienna, AT. (Free) registration open: https://www.appn.at/3rdappn/ Confirmed speakers (in alphabetical order): Opening speech: Christian Obinger, Vice Rector for Research, University of Natural Resources and Life Sciences (BOKU) Clement Atzberger, Head of Institute for Surveying, Remote Sensing and Land Information, University of Natural Resources and Life Sciences and GreenSense GmbH, AT “Determining crop traits through multi-spectral data” Helge Aasen, ETH Zürich, Dep. of Environmental System Science, CH “Low-altitude / high-resolution remote sensing for field-phenotyping” Ittai Herrmann, The Hebrew University of Jerusalem, R.H. Smith Faculty of Agriculture, Food and Environment, IL “Field crops phenotyping (disease, water status and yield) by spectral remote and proximal sensing” Jan F. Humplík, Palacky University Olomouc, CZ “Field plant phenotyping using UAV LiDAR system: current state and first experiences.” Pieter Clauw, Gregor Mendel Institute of Molecular Plant Biology (GMI), AT “Combining growth chamber simulations and field experiments to tackle temperature adaptation in Arabidopsis thaliana” Please feel free to share & spread the word! Looking very much forward to meeting you, Gernot Bodner, Boris Rewald (local organizers) & Jakub Jez [signature_381824586]<http://www.appn.at/>

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Two OPEN POSITIONS @VBCF_PlantS
by Jez,Jakub 22 Mar '19

22 Mar '19

Dear friends, We have two open full-time (38h) positions at our facility! DATA SCIENTIST PHENOTYPING SPECIALIST Please visit the VBC career homepage for details: https://www.viennabiocenter.org/vbcf-jobs/ In case of interest or questions please feel free to drop by my office for a chat. Best, Jakub [VBC Logo] Jakub Jeż Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77 090<tel:+43%20664%208084%2077%20090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at>

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FW: Waste bins in PlantS Facility
by Auer, Anneliese 19 Mar '19

19 Mar '19

Dear all, a short reminder of "General Plant Rules": Do not fill the waste bins with orange autoclave bag more than half full. Full bins with wet soil are really too heavy for our waste management staff! Thank you for your cooperation. Best Anneliese Anneliese Auer Senior Plant Facility Technician Gregor Mendel Institute of Molecular Plant Biology GmbH Dr. Bohr-Gasse 3, 1030 Vienna, Austria Phone: +43 1 79044 9990 anneliese.auer(a)gmi.oeaw.ac.at http://www.gmi.oeaw.ac.at

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3rd APPN meeting SAVE-THE-DATE!
by Jez,Jakub 27 Feb '19

27 Feb '19

Dear friends! We have just fixed the date and location for the 3rd Austrian Plant Phenotyping Network (APPN) meeting! Date: Thursday, 13th June 2019 Venue: BOKU Vienna, Festsaal, main building Please save the date! Last year we put emphasis on root phenotyping (https://www.appn.at/2ndappn_eppn2020-2/) this year the main focus will be (although not exclusively) on FIELD PHENOTYPING. Other plant phenotyping topics (controlled environments, root phenotyping and others) will be covered by the respective sessions and based on the received abstracts. Details, and the registration page will be open soon on www.appn.at<http://www.appn.at> Looking forward to receiving your abstracts and meeting you in June! Best regards, Gernot Bodner, Boris Rewald (local organizers) & APPN board [signature_1677033384]<http://www.appn.at/>

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Open position @VBCF Plants: Bioinformatician/Data Analyst (full-time)
by Jez,Jakub 21 Feb '19

21 Feb '19

Dear friends, We have opened a position for a Bioinformatician/Data Analyst to join our PlantS team and support the construction and validation of PHENOPlant and help us build our HT plant phenotyping data analysis pipelines. In between large-scale HT phenotyping projects, and within free capacities, the candidate is intended also to work on other projects for our users (non-strictly plant phenotyping related projects). Please help us (and maybe also yourself) to find an excellent candidate to support your research and spread the word: https://www.viennabiocenter.org/vbcf-jobs/ https://twitter.com/VBCF_PlantS/status/1098153265253023744 https://www.linkedin.com/feed/update/urn:li:activity:6504015287585771520 https://www.viennabiocenter.org/about/news/large-infrastructure-project-phe… Thank you very much. Best, Jakub [VBC Logo] Jakub Jeż Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77 090<tel:+43%20664%208084%2077%20090> jakub.jez(a)vbcf.ac.at<mailto:jakub.jez@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at<https://www.vbcf.ac.at>

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