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Construction works @PlantS Facility GMI and MFPL
by Jez,Jakub Nov. 29, 2019

Nov. 29, 2019

Dear all, Next week small construction works are planned that might slightly affect the daily operation (mostly accessibility/corridor) of the Facility. In the next weeks we will also need to shut down phytotron #22 and #23 (one by the other) for a significant amount of time. No other phytotrons will be affected! GMI -1: Tuesday 3rd Dec and Wednesday 4th Dec Replacement of a pipe in the corridor (this particular pipe is not at all related to the operation of our Facility). MFPL 8th floor: 2.5 weeks from the 2nd December on CO2 System installation in #22 and #23 In case of any questions please do not hesitate to contact me. 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_589218479] 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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NEW EXPERTISE @PlantS: Machine Learning, Data Analysis, Basic Statistics, Data Visualization and Scripting
by Jez,Jakub Nov. 21, 2019

Nov. 21, 2019

Dear all, In the light of the upcoming high-throughput plant phenotyping infrastructure (PHENOPlant) and also the closure of the BioComp facility, we have extended and strengthened our service portfolio by providing expertise in: * Machine Learning (e.g. image segmentation & classification) * Data analysis and basic statistics (not strictly phenotyping data related) * Data Visualization * Tools/scripting (e.g. script-based workflow automation: experiment design, sample randomization, sample identification (QR codes), etc.) * Small, in-house hardware programming and electronics projects (see PHENOBox) in collaboration with the workshop powered by @Stewart,Ethan<mailto:ethan.stewart@vbcf.ac.at> (Staff Scientist) & @Seitner,Sebastian<mailto:sebastian.seitner@vbcf.ac.at> (Software Engineer; programmer of the PHENOBox). Supported languages: Python, C, R, Java, JavaSript and TypeScript. Please do not hesitate to contact me for further information and requests. Best, Jakub.

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GMI Seminar - Ethan Stewart: “The application of a deep learning approach for quantitative disease phenotyping in drone images”
by Jez,Jakub Sept. 13, 2019

Sept. 13, 2019

Dear all! this is a kind reminder on Ethan’s GMI Seminar today 11:30, @ GMI OSR! See you soon, Jakub “ Ethan Stewart, Plant Sciences, Vienna BioCenter Core Facilities<https://www.viennabiocenter.org/facilities/plant-sciences/> “The application of a deep learning approach for quantitative disease phenotyping in drone images” Friday, 13 September 2019, 11:30am @ GMI Orange Seminar Room. “ From: Jakub Jez <jakub.jez(a)vbcf.ac.at> Date: Monday, 2. September 2019 at 15:49 To: "Gsur,Martina" <martina.gsur(a)gmi.oeaw.ac.at>, imp imba gmi vbcf <impimbagmivbcf(a)imp.ac.at> Cc: "Steurer,Manuela" <manuela.steurer(a)imp.ac.at>, "'Eva Schweng (ESchweng(a)cemm.oeaw.ac.at)'" <eschweng(a)cemm.oeaw.ac.at>, "sandor.fueloep(a)mfpl.ac.at" <sandor.fueloep(a)mfpl.ac.at>, "Stewart,Ethan" <ethan.stewart(a)vbcf.ac.at> Subject: FW: GMI Seminar - Ethan Stewart, 13.9.2019 Dear all, I would like to take the chance and add, that Ethan recently started at the PlantS Facility as a Staff Scientist. Ethan will take over the hands-on responsibility for the present and future (FFG PHENOPlant Infrastructure) plant phenotyping services. Moreover, Ethan will strengthen our data analysis service and extend our phenotyping service by deep learning approaches. Looking forward to meeting you next Friday. Best regards, Jakub [Image removed by sender. 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> [Image removed by sender. signature_1455416007] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021! From: "Gsur,Martina" <martina.gsur(a)gmi.oeaw.ac.at> Date: Monday, 2. September 2019 at 15:35 To: GMI-IMBA-IMP <GMI-IMBA-IMP(a)gmi.oeaw.ac.at> Cc: "Steurer,Manuela" <manuela.steurer(a)imp.ac.at>, "'Eva Schweng (ESchweng(a)cemm.oeaw.ac.at)'" <eschweng(a)cemm.oeaw.ac.at>, "sandor.fueloep(a)mfpl.ac.at" <sandor.fueloep(a)mfpl.ac.at> Subject: GMI Seminar - Ethan Stewart, 13.9.2019 Dear all, Please let me know if you are interested in speaking with Ethan next week Friday. Best, Martina ___________________________________ Dear all, another GMI seminar to announce for September, hosted by Kelly Swarts: Ethan Stewart, Plant Sciences, Vienna BioCenter Core Facilities<https://www.viennabiocenter.org/facilities/plant-sciences/> “The application of a deep learning approach for quantitative disease phenotyping in drone images” Friday, 13 September 2019, 11:30am @ GMI Orange Seminar Room. Best, Martina

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SD phytotron #18
by Jez,Jakub Sept. 13, 2019

Sept. 13, 2019

Dear all, We would need the MFPL SD phytotron #18 for other environmental conditions (next 4 months). This particular phytotron is not being used and empty for the last (~4) months. Do you plan to use SD conditions in the near future? Thanks and best, Jakub

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Today: PHENOBox booth VBC Technology day!
by Jez,Jakub Sept. 3, 2019

Sept. 3, 2019

Dear all, Our summer students are presenting the PHENOBox today at our booth at the VBC technology day (IMP foyer). Visit us today at 3pm for a coffee or 6pm for finger food if you are interested in side-view phenotyping of crop plants and agar-plate based phenotyping of shoots and roots. See you! Best, Jakub Sent from a "smart"phone - please excuse typos.

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3rd APPN Meeting presentations published!
by Jez,Jakub July 12, 2019

July 12, 2019

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 July 12, 2019

July 12, 2019

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 July 4, 2019

July 4, 2019

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 May 29, 2019

May 29, 2019

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 May 9, 2019

May 9, 2019

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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