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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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Clogged shelf in PlantS Facility
by Auer,Anneliese July 17, 2020

July 17, 2020

Dear all, Please don`t dump dirty water with soil into the shelf. Otherwise the drain will be blocked! Best, Anneliese

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Personal changes VBCF PlantS team
by Jez,Jakub July 6, 2020

July 6, 2020

Dear all, I would like to inform you that Jolanta Ambroz-Kumorowski left the VBCF and is no longer responsible for the VBCF phytotrons located at the MPL. @Auer,Anneliese<mailto:anneliese.auer@vbcf.ac.at> will take over Jolanta’s duties and responsibilities. The MPL cleaning company (Kling Wagenhofer) will take care of the dirty trays. This task will take place at a very early time of the day (at least for me) thus not interfering with your soil work and pot preparations. Please continue contacting us via plants(a)vbcf.ac.at<mailto:plants@vbcf.ac.at> Please do not hesitate to contact me in case of any questions, comments or complains. 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 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!

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VBCF PlantS office moved!
by Jez,Jakub May 20, 2020

May 20, 2020

Dear all, our main office moved from the VBC2 PG12 to the oldnew VBC6 building (old IMP), 2nd floor, room 283. The easiest way to get to us is via the IMBA blue floor. After entering VBC6 it is the first office on the left side. Please note that we are still mainly working in home office mode but will return soon slowly back to VBC. Best regards, PlantS Team

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VBCF PlantS: gradual start of operation - rules & measures - booking of working rooms
by Jez,Jakub April 16, 2020

April 16, 2020

Dear all, In the light of the ongoing gradual ramp up of research activities at the VBC and in line with the current regulations of the VBCF and the respective VBC institutes, we would like to update you on the rules and measures that were recently implemented at the VBCF Plant Sciences Facility. 1. One person one room rule: only one person is allowed to work in each room at each time. This includes all soil working rooms, plant handling rooms, phytotrons and glasshouse cabins but also GMI cell culture rooms. * Please book your activities in advanced! New booking items where implemented in the respective booking system for all soil- and plant working rooms as well as for the GMI cell culture rooms: GMI working rooms and cell culture rooms can be booked here: https://orgt.vbc.ac.at/#cal-win (section Lab Services; VPN connection needed) MFPL working rooms can be booked in the general PlantS Phytotron booking system: https://www.intranet.mfpl.ac.at/vbcf_login/ Note for MFPL bookings: Equipment category is “Plant Sciences Facility (VBCF) – Rooms” (it was not possible to implement them in the Phytotrons category). In case you don’t have access to the PlantS booking system, please contact your TA OR @Auer,Anneliese<mailto:anneliese.auer@vbcf.ac.at> via mail for booking. Please keep a 15min break between the bookings to allow for sufficient air exchange (aerosols in the air). Please don’t book the rooms longer then needed; maximum booking time is 2h per room, per person and per day. * When passing by another person, please coordinate to maintain a minimal distance of 2m. * No activities are allowed to happen in the corridors of the Facility (e.g. plant work on trolleys/desks). * Before you enter a phytotron take a look through the window in the door; especially in the case of shared phytotrons! * Coordinate the access to phytotrons which are exclusively assigned to your research group internally. 1. Please wear lab coats, gloves and mask at all times. * Gloves will be provided in front of each entrance to the PlantS Facility. * Lab coats and mask are provided centrally by the respective institute. 1. The workplace must be disinfected before and at the end of work. * Please use the dedicated surface disinfectant and/or 70% EtOH provided by the Facility 1. Service availability * The PlantS premises, infrastructure (phytotrons, working rooms,…) and consumables are available to you in compliance with the current EHS and above mentioned PlantS Facility rules. * PlantS services are only available in compliance with the current EHS and PlantS Facility rules. Please contact us in advanced for concrete information on individual services. * Remote services e.g. image- and data analysis, phytotron programming are operational. All above mentioned rules and measures are valid until further notice and in line and in addition to the valid rules, regulations and measures set by the government, the VBCF and the respective VBC Institutes! Get in touch with us in case of any questions. Thank you for your cooperation; stay healthy! Yours, VBCF 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_776704168] FFG PHENOPlant<https://www.viennabiocenter.org/projects-grants/phenoplant/>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

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[APPN] 4th APPN meeting - From Cell to Field - June 25th, VBC, Vienna AT
by Jez,Jakub March 13, 2020

March 13, 2020

! This is not a cancelation but an INVITATION: https://appn.at/4thappn/ Dear colleagues and friends, It is our pleasure to invite you to the 4th Austrian Plant Phenotyping Network (APPN) Conference featuring “From Cell to Field” with the major focus on Pattern Recognition, Machine Learning and Modelling in the context of Plant Phenotyping. Joint Organization by the University of Vienna, VBCF and OAGM The meeting will take place on June 25, 2020 at the Vienna BioCenter (Free) registration open: https://appn.at/4thappn/ Confirmed speakers (in alphabetical order): Sven Fahrner, ESFRI-EMPHASIS, DE Kristina Gruden, NIB, SI Verena Ibl, Mosys, University of Vienna, AT Astrid Junker, IPK Gatersleben, DE Thomas Nägele, LMU München, DE Peter M. Roth, Graz University of Technology , AT Wolfram Weckwerth, Mosys, Uni Vienna, AT Please feel free to share & spread the word! Looking very much forward to meeting you, Stefanie WIenkoop, Markus Teige and Jakub Jez

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Operation VBCF PlantS facility
by Jez,Jakub March 13, 2020

March 13, 2020

Dear all, due to the given design and setup of the Facility (remote control) and taken measures we will be able to keep up the main operation of the phytotrons and most of our (digital) services (…from today’s point of view). Please find important information, taken measures, reaction times and contact details summarized below: 1. We have increased the stock of consumables to avoid ordering and deliveries in the upcoming 3-4 weeks. 2. Anneliese and Jolanta will reduce their on-campus presence to a necessary minimum adapting to the actual workload of the research groups 3. Phytotron operation and control incl. alarms and repairs will continue via remote control/home-office mode by Anneliese and Jakub 4. Maintenance and repairs will continue, as usual 24/7, by our external partner Incotec-Cooling GmbH and GMI/IMBA Haustechnik 5. Image- and data analysis service (Ethan) as well Software development & PHENOBox (Sebastian) will continue in home-office mode 6. Please direct your requests, as usual, to: plants(a)vbcf.ac.at<mailto:plants@vbcf.ac.at>; in urgent cases (additionally to the mail!) call 1. Jakub: +43664 8084 77 090 and/or 2. Anneliese: +43664 80 51 53 9101 7. In very urgent cases the PlantS team will arrive at the campus within 1-2h latest. Please contact me in case of any questions!! 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> [signature_40916913] FFG PHENOPlant<https://projekte.ffg.at/projekt/3148498>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

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Waste Bins in PlantS Facility
by Auer,Anneliese March 9, 2020

March 9, 2020

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 too heavy for our waste management staff! And do not collect waste in orange autoclave bags outside of waste bins, please ask me for extra bins if you need them. 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 [cid:gmi_48f983b7-0679-4d21-99bc-bda376e5bf6b.png]

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