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

[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

1 0

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!

1 0

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]

1 0

CO2 atmosphere control @PlantS & GMI GeneGun move to MFPL
by Jez,Jakub March 5, 2020

March 5, 2020

Dear all, We have completed the installation of the CO2 control system in phytotron #22 and #23 (MFPL location). CO2 concentrations of ambient/400ppm up to 2000ppm can be simulated with a precision of +/- 5ppm. Higher values can also be set upon special request. Get in touch with us for project requests. The GeneGun, which is currently located @GMI room #8.18, will be moved tomorrow morning to the MFPL PlantS Lab. Please contact me in case of any questions. 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_1470311651] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

1 0

HT Phenotyping Phytotron available!
by Jez,Jakub Jan. 10, 2020

Jan. 10, 2020

Dear all, Our high-throughput plant phenotyping phytotron is again available from February on till end of April! [cid:image001.gif@01D5C7C2.4D7761F0] This particular phytotron is capable of providing various abiotic stresses like cold (-15C), drought, waterlogging, variable spectral light conditions (LED) and complex environmental simulations (dynamic simulations of temperature and rel. humidity). We provide full HT phenotyping service – from the seed via image analysis to data analysis and statistics. https://www.viennabiocenter.org/facilities/plant-sciences/ Get in touch with us for more information and project requests. 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_295421225] FFG PHENOPlant<https://www.ffg.at/sites/default/files/allgemeine_downloads/strukturprogram…>: Austrias 1st multi-sensor, high-throughput plant phenotyping infrastructure launching 2021!

1 0

PLANT STRESS NEWS! Please read!
by Jez,Jakub Dec. 23, 2019

Dec. 23, 2019

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!

2 5

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!

1 0

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.

1 0

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

1 0

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

3 2