- plants-user - lists.vbcf.ac.at

High-troughput plant phenotyping 360° video #PHENOPlant @VBC
by Jez,Jakub Aug. 23, 2022

Aug. 23, 2022

Dear friends, In case you didn’t get the chance yet to visit the newly established VBCF high-throughput plant phenotyping infrastructure #PHENOPlant here is as short 360° video from the point-of-view of a plant. Enjoy watching! https://twitter.com/VBCF_PlantS/status/1562005727534776320 https://www.linkedin.com/feed/update/urn:li:activity:6967774727557820416/ Please help to spread the news. Thanks, cheers, 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> [A picture containing text, indoor, wall Description automatically generated] FFG PHENOPlant<https://www.viennabiocenter.org/facilities/plant-sciences/phenoplant/>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

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VBCF PlantS: Transistion to new booking system PPMS
by Seitner,Sebastian July 18, 2022

July 18, 2022

Dear all, as announced in a previous email we switched to Stratocore PPMS as a booking system for our Phytotrons today. From now on the old system in the MPL intranet will not be available anymore. You can reach PPMS via https://booking.vbc.ac.at For an explanation on how to use PPMS to book our chambers use the tutorial at the following link: https://www.vbcf.ac.at/myvbcf-sim/stratocoreppms-quick-start-guide-plants/ All previous bookings have successfully been transferred to the new system, so no action is necessary on your side. We know that the system is not perfectly suited for our use case, but it was necessary to migrate to a new system and as PPMS was already established we tried to use it as best as we could. If you have any issues or questions do not hesitate to contact us via plants(a)vbcf.ac.at<mailto:plants@vbcf.ac.at> For MPL or external users (e.g. University of Vienna): Please follow the outlined steps below to gain access to the booking system. This is necessary to synchronize your data and permissions. It might be the case that you are not able to book chambers until the next day. MPL Users * visit https://booking.vbc.ac.at * choose facility VBCF PlantS * click “Continue to Login” * click the MaxPerutzLabs Logo * login with your MaxPerutzLabs login credentials (the same you also use for the MaxPerutzLabs intranet) * fill out the user request form (most important: Group! All other fields are optional) * click send external Users * visit https://booking.vbc.ac.at * choose facility VBCF PlantS * click “Continue to Login” * click button “External login / registration” at the bottom * click “Register” at the bottom * fill out form completely and click Register at the bottom Best regards, Sebastian Seitner [signature_459486170] Sebastian Seitner Software Engineer, Plant Sciences Facility T +43 1 7962324 9836<tel:+43179623249836> sebastian.seitner(a)vbcf.ac.at<mailto:sebastian.seitner@vbcf.ac.at> Vienna BioCenter Core Facilities GmbH Dr. Bohr-Gasse 3 1030 Vienna Austria www.vbcf.ac.at/plants<https://www.vbcf.ac.at/plants> [A picture containing text, indoor, wall Description automatically generated] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launched 2021!

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VBCF PlantS: NEW BOOKING SYSTEM (Stratocore PPMS) - 18th July 2022
by Jez,Jakub July 7, 2022

July 7, 2022

Dear all, on Monday, the 18th July 2022, we will switch our present booking system (MPL intranet) to Stratocore PPMS. PPMS is already in successful operation at e.g. GMI, IMP, VBCF, MPL and ISTA. All present bookings from the MPL Intranet will be transferred to PPMS by us, and there is no action on your side needed. Detailed instructions on how to access and use the new booking system will follow soon, and in time. Pre-warning: The PPMS is not 100% suited to deal with our use case (trays in phytotrons; and long-term bookings) as it was originally designed for booking of microscopes, rooms, etc. on an hourly basis. However, we did our best to establish some painless workarounds to make it fit our special needs. The booking procedures incl. the workarounds will be explained to you in detail soon. 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> [A picture containing text, indoor, wall Description automatically generated] FFG PHENOPlant<https://www.viennabiocenter.org/facilities/plant-sciences/phenoplant/>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

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Research Fellow - High-Throughput Plant Phenotyping
by Jez,Jakub March 18, 2022

March 18, 2022

FYI, best, Jakub. From: Ittai Herrmann <Ittai.Herrmann(a)mail.huji.ac.il> Date: Thursday, 17. March 2022 at 15:36 To: Jez,Jakub <jakub.jez(a)vbcf.ac.at> Subject: Research Fellow - High-Throughput Plant Phenotyping Hi Jakub, Attached is a call for a Research Fellow in High-Throughput Plant Phenotyping, It would be great if you know a relevant candidate and can forward this to her/im. The call is for a Research Fellow in the Nanyang Technological University (NTU) in collaboration with the Hebrew University of Jerusalem (HUJI). This is an Israeli-Singaporian project incorporating a unique multimodal indoors remote sensing HTTP system with whole plant and environmental sensing system. All data is to be fused and analyzed with AI techniques to optimize yield of indoor crops under solid and hydroponic substrates. The successful candidate will take part in developing and starting the data collection from this unique HTTP system and should be a constructive team member while maintaining independent research. For more information please contact Ittai Herrmann - Ittai.Herrmann(a)mail.huji.ac.il<mailto:Ittai.Herrmann@mail.huji.ac.il> The aim is to start late summer (about September 2022) Sincerely, Ittai -- Ittai Herrmann, PhD The Plant Sensing Laboratory The Robert H. Smith Institute for Plant Sciences and Genetics in Agriculture The Robert H. Smith Faculty of Agriculture, Food and Environment The Hebrew University of Jerusalem P.O. Box 12, Rehovot 7610001, ISRAEL Office: +972-8-9489757 Mobile: +972-52-3947255 Fax: +972-8-9489918 Lab: +972-8-9489958 Email: ittai.herrmann(a)mail.huji.ac.il<mailto:alon.samach@mail.huji.ac.il> Site: http://departments.agri.huji.ac.il/plantscience/people/Ittai_Herrmann ORCID ID: https://orcid.org/0000-0003-1136-1883 https://www.researchgate.net/profile/Ittai_Herrmann

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Workshop Computer Vision and Pattern Analysis Across Domains
by Jez,Jakub Sept. 9, 2021

Sept. 9, 2021

Austrian Association for Pattern Recognition (OAGM) workshop on Computer Vision and Pattern Analysis Across Domains 24.-25. November 2021, St. Pölten, Austria Details and registration: https://workshops.aapr.at/ 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> [A picture containing text, indoor, wall Description automatically generated] FFG PHENOPlant<https://www.viennabiocenter.org/facilities/plant-sciences/phenoplant/>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021! Subject: [OAGM] [OAGM Workshop 2021] Deadline extension to September 24th Dear colleagues, please note that we have extended the deadline for the annual OAGM workshop by two weeks to Sept. 24th. Aside from that, we have fixed the lineup of invited speakers, check https://workshops.aapr.at/ for details. Best wishes, Markus Seidl & Matthias Zeppelzauer _______________________ FH-Prof. DI Dr. Markus Seidl Academic Director of Creative Computing (BA) Fachhochschule St. Pölten GmbH Matthias Corvinus-Straße 15, 3100 St. Pölten T: +43/2742/313 228 – 245 F: +43/2742/313 228 – 609 E: markus.seidl(a)fhstp.ac.at<mailto:markus.seidl@fhstp.ac.at> I: http://mc.fhstp.ac.at/people/markus-seidl ORCID: https://orcid.org/0000-0002-7966-3602 FN 146616m, LG St. Pölten, DVR 1028669F

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FW: Question, Job offer: Post-Graduate Position
by Jez,Jakub Sept. 6, 2021

Sept. 6, 2021

Open Post-Graduate Position in Physiological and Biochemical responses to drought stress at the BFW (https://www.bfw.gv.at/ ) in Schönbrunn/Vienna. This project is also associated with our new HT plant phenotyping infrastructure PHENOPlant! Details see attachment. Best, Jakub. From: Vanloo Marcela <marcela.vanloo(a)bfw.gv.at> Date: Thursday, 26. August 2021 at 02:57 To: Jez,Jakub <jakub.jez(a)vbcf.ac.at> Cc: Trujillo-Moya Carlos <carlos.trujillo-moya(a)bfw.gv.at> Subject: WG: Question, Job offer: Post-Graduate Position Dear Jakub! We are offering a new job opportunity: Post-Graduate Position in Physiological and Biochemical responses to drought stress associated also to the PHENOPlant. Could you spread the word and when possible to post it on Biocenter "job offers"? Thank you very much. ? Yours sincerely,? Marcela ************************************************************************* Dr. Marcela van Loo Bundesforschungs- und Ausbildungszentrum für Wald, Naturgefahren und Landschaft (BFW) Federal Research Centre for Forests, Natural Hazards and Landscape (BFW) Institut für Waldbau, Waldwachstum und Genetik / Department of Forest Growth, Silviculture and Genetics Abteilung für Herkunftsforschung und Züchtung / Unit of Provenance Research and Breeding A-1130 Wien, Seckendorff-Gudent-Weg 8, Austria Tel: +43 / 1 / 87838 / 1349 E-mail: marcela.vanloo(a)bfw.gv.at URL: http://bfw.ac.at<http://bfw.ac.at/> **************************************************************************

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Free, free slots in PHENOPlant!
by Jez,Jakub Aug. 18, 2021

Aug. 18, 2021

Dear all, In parallel to our currently running large-scale FFG pilot experiment, we have some free capacities in the small sample loop to run parallel small-scale experiments. So, if you are interested in phenotyping your plants (small-scale, preliminary experiment, proof of concept style), please drop me a mail. PHENOPlant can deal with various sample types: from multi-well plates (6, 12 and 24well) via Arabidopsis up to tall (crop) plants (max plant height 70cm). Available sensors: * RGB (top- & side-view) * 3D laser scan * PAM chlorophyll fluorescence * Fluorescence imaging of marker proteins (wtGFP, eGFP, DAPI, YFP, RFP, Cy3, SYBR Green and many more). * LWIR thermal imaging * Hyperspectral imaging (VNIR and SVIR) * Automated weighing & watering stations (two tanks each). More info: https://www.viennabiocenter.org/vbcf/plant-sciences/phenoplant/ Questions are welcome. First come first surf 🤙 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> [A picture containing text, indoor, wall Description automatically generated] FFG PHENOPlant<https://www.viennabiocenter.org/facilities/plant-sciences/phenoplant/>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

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APPN/GMI Seminar - High-throughput, multi-sensor plant phenotyping (VBCF PHENOPlant project)
by Jez,Jakub May 28, 2021

May 28, 2021

Dear APPN member! I hope you came well and healthy through the (still ongoing) corona crisis. As you might have heard, we are very close to the end of the FFG PHENOPlant project, expecting the commissioning of the infrastructure in the upcoming weeks. (For more regular updates and pictures please visit our Twitter and LinkedIn channel.) Right on time with the re-opening steps in Austria, I would like to invite you to a seminar on high-throughput plant phenotyping by Dr. Klára Panzarová (PSI Research Center) which will take place this Friday, 28th May 2021, 11:30am via Zoom. Klara will talk about the PHENOPlant infrastructure with focus on the incorporated high-tech sensors and the resulting potential biological applications for basic and applied plant research. In particular, following sensors will be presented and discussed: PAM Chlorophyll Fluorescence imaging, LWIR thermal imaging, RGB imaging, 3D imaging (scan) and hyperspectral imaging (VNIR & SWIR). This seminar intends to introduce PHENOPlant capabilities and functionality to the APPN community, but also to stimulate new research ideas and projects that are now feasible also in Austria. But also, to further educate young scientist; so, please feel free to share this invitation with your students and your network. Dr. Klára Panzarová, PSI – Photon Systems Instruments, spol. s r.o. "VBCF PHENOPlant project: Multi-sensor, high-throughput plant phenotyping infrastructure - potential applications in basic and applied plant research". Friday, 28th May 2021, 11:30am on Zoom https://us02web.zoom.us/j/89561047758?pwd=VjZhOFlSQzRaekpXV0tybHhJTGQ3UT09 Meeting ID: 895 6104 7758, Passcode: 292115 Hope to see many of you. Stay safe and healthy, 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> [A picture containing text, indoor, wall Description automatically generated] FFG PHENOPlant<https://www.viennabiocenter.org/facilities/plant-sciences/phenoplant/>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021! From: "Gsur,Martina" <martina.gsur(a)gmi.oeaw.ac.at> Date: Thursday, 20. May 2021 at 15:26 Cc: Jakub Jez <jakub.jez(a)vbcf.ac.at> Subject: Seminar - VBCF PHENOPlant project Dear all, You are cordially invited to a seminar hosted by Jakub Jez, VBCF, Plant Sciences Facility: Dr. Klára Panzarová, PSI – Photon Systems Instruments, spol. s r.o. "VBCF PHENOPlant project: Multi-sensor, high-throughput plant phenotyping infrastructure - potential applications in basic and applied plant research". Friday, 28th May 2021, 11:30am on Zoom https://us02web.zoom.us/j/89561047758?pwd=VjZhOFlSQzRaekpXV0tybHhJTGQ3UT09 Meeting ID: 895 6104 7758, Passcode: 292115 Best wishes, Martina

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Seminar - VBCF PHENOPlant project
by Jez,Jakub May 20, 2021

May 20, 2021

Dear all, You are cordially invited to a seminar hosted by Jakub Jez, VBCF, Plant Sciences Facility: Dr. Klára Panzarová, PSI – Photon Systems Instruments, spol. s r.o. "VBCF PHENOPlant project: Multi-sensor, high-throughput plant phenotyping infrastructure - potential applications in basic and applied plant research". Friday, 28th May 2021, 11:30am on Zoom https://us02web.zoom.us/j/89561047758?pwd=VjZhOFlSQzRaekpXV0tybHhJTGQ3UT09 Meeting ID: 895 6104 7758, Passcode: 292115 Best wishes, Martina

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New soil available for testing - Klasmann Substrate 2
by Jez,Jakub Dec. 16, 2020

Dec. 16, 2020

Dear all, as you know, we had some troubles with the soil (Gramoflor 2006) und subsequent plant stress symptoms (anthocyanin accumulation in leaves). It turned out that this was mainly caused by the lack of nutrients, especially of phosphorous, (details please see mail below). The last weeks we did successfully test a very promising substrate: “Klasmann – Deilmann Substrat 2” with excellent references (e.g. ETH Zürich and PSI HT phenotyping platforms). This substrate comes with a very balanced composition, structure/texture and nutrient mix. But it does not only look good on paper; our tests with Arabidopsis (Col-0 and numerous accessions/mutants; thx Tesi, Schlögelhofer group) showed that no stress symptoms appeared (under LED and fluo-tube light). Furthermore, it does not require sieving before potting. This Klasmann Substrate 2 is now available for you at the soil room for testing! Your feedback is of great importance and very much appreciated! We are available as usual for your questions, comments and complaints. Best regards, 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 7 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> [A close up of a tree Description automatically generated] FFG PHENOPlant<https://www.viennabiocenter.org/projects-grants/phenoplant/>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021! From: Jakub Jez <jakub.jez(a)vbcf.ac.at> Date: Thursday, 28. November 2019 at 11:03 To: GMI All <gmi.all.intern(a)gmi.oeaw.ac.at>, VBCF Pant Sciences Facility user mailing list <plants-user(a)lists.vbcf.ac.at> Cc: "VBCFplants.GRP" <plants(a)vbcf.ac.at> Subject: PLANT STRESS NEWS! Please read! 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!

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