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PLANT STRESS NEWS! Please read!

by Jez,Jakub

Dear friends, In the last weeks/months we have been investigating the plant stress issue, mainly focusing on the LED light spectrum. Always comparing to the fluorescent tube standard. Surprisingly, also the fluorescent tube setup shows same plant stress issues! Which was not the case in the very beginning when we have tested and decided for the new type of soil. See picture attached to this mail: Phytotron: #21 Soil: Gramoflor2006; not sieved; with perlite Light: Fluorescent tubes; LD Watering: Flooding twice a week Left side of the tray: WUXAL treated plants (once, after 1 month, 2ml/L) Right side of the tray: untreated plants Our new hypothesis focuses on the soil. In particular, on the soil composition and the available nutrients. From today’s point of view, it looks like the composition of the soil might have changed over the last months (without informing us); but this needs further investigation. The automated watering system (flooding) also eventually contributes negatively to the problem by washing out nutrients; twice a week. Also sieving might be suboptimal. Red leaves are known to be a symptom for Phosphor/Phosphate deficiency. We are in touch with the soil supplier and with APPN soil scientist from the BOKU to find a long-term solution. As a quick fix * you can fertilize your plants with WUXAL fertilizer which is available in the Facility (once after ~1month; 2ml/L; watering from the top). * Use a long-term fertilizer (OSMOCOTE) * Use the old type of soil ED63 Please contact Anneliese in case of questions for the quick fix. We will keep you posted on further steps and present you soon our final results and the long-term solution. Looking forward to your valuable feedback on your quick-fix results. Best wishes, yours PlantS Team [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_949803173] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

Nov. 28, 2019

NEW EXPERTISE @PlantS: Machine Learning, Data Analysis, Basic Statistics, Data Visualization and Scripting

by Jez,Jakub

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.

Nov. 21, 2019

GMI Seminar - Ethan Stewart: “The application of a deep learning approach for quantitative disease phenotyping in drone images”

by Jez,Jakub

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

Sept. 13, 2019

Re: [Plants-user] SD phytotron #18

by Andreas Bachmair

Dear Jakub, I have no plans to book this phytotron. So change does not affect me. Sincerely, Andreas > On 12.09.2019, at 15:57, Jez,Jakub <jakub.jez(a)vbcf.ac.at> wrote: > > 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 > _______________________________________________ > plants-user mailing list > plants-user(a)lists.vbcf.ac.at > https://www.vbcf.ac.at/mailman/listinfo/plants-user

Sept. 13, 2019

Re: [Plants-user] SD phytotron #18

by Peter Schlögelhofer

…no plans. many thanks for asking. feel free to use. best regards, peter > On 12 Sep 2019, at 15:57, Jez,Jakub <jakub.jez(a)vbcf.ac.at> wrote: > > 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 > _______________________________________________ > plants-user mailing list > plants-user(a)lists.vbcf.ac.at <mailto:plants-user@lists.vbcf.ac.at> > https://www.vbcf.ac.at/mailman/listinfo/plants-user <https://www.vbcf.ac.at/mailman/listinfo/plants-user> Dr. Peter Schlögelhofer Department of Chromosome Biology Max Perutz Labs University of Vienna Dr. Bohr-Gasse 9 1030 Vienna Austria Phone: +43 1 4277 56240 Email: peter.schloegelhofer(a)univie.ac.at

Sept. 12, 2019

SD phytotron #18

by Jez,Jakub

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

Sept. 12, 2019

Today: PHENOBox booth VBC Technology day!

by Jez,Jakub

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.

Sept. 3, 2019

3rd APPN Meeting presentations published!

by Jez,Jakub

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!

July 12, 2019

Hydroponics+Arabidopis=Araponics

by Jez,Jakub

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!

July 12, 2019

PHENOBox upgrade to 12x12 agar-plates (screening of seedlings and roots)

by Jez,Jakub

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!

July 4, 2019