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

Program 3rd APPN Meeting published!

by Jez,Jakub

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>

May 29, 2019

3rd APPN meeting - Field Phenotyping and Remote Sensing, 13th June, BOKU, Vienna, AT

by Jez,Jakub

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

May 9, 2019

3rd APPN meeting - Field Phenotyping and Remote Sensing, 13th June, BOKU, Vienna, AT

by Jez,Jakub

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/ Confirmed speakers (in alphabetical order): Opening speech: Christian Obinger, Vice Rector for Research, University of Natural Resources and Life Sciences (BOKU) 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” 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, Palacky University Olomouc, CZ “Field plant phenotyping using UAV LiDAR system: current state and first experiences.” Pieter Clauw, Gregor Mendel Institute of Molecular Plant Biology (GMI), AT “Combining growth chamber simulations and field experiments to tackle temperature adaptation in Arabidopsis thaliana” Please feel free to share & spread the word! Looking very much forward to meeting you, Gernot Bodner, Boris Rewald (local organizers) & Jakub Jez [signature_381824586]<http://www.appn.at/>

March 25, 2019

Two OPEN POSITIONS @VBCF_PlantS

by Jez,Jakub

Dear friends, We have two open full-time (38h) positions at our facility! DATA SCIENTIST PHENOTYPING SPECIALIST Please visit the VBC career homepage for details: https://www.viennabiocenter.org/vbcf-jobs/ In case of interest or questions please feel free to drop by my office for a chat. Best, Jakub [VBC Logo] Jakub Jeż Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77 090<tel:+43%20664%208084%2077%20090> 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>

March 22, 2019

FW: Waste bins in PlantS Facility

by Auer, Anneliese

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 really too heavy for our waste management staff! 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

March 19, 2019

3rd APPN meeting SAVE-THE-DATE!

by Jez,Jakub

Dear friends! We have just fixed the date and location for the 3rd Austrian Plant Phenotyping Network (APPN) meeting! Date: Thursday, 13th June 2019 Venue: BOKU Vienna, Festsaal, main building Please save the date! 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. Other plant phenotyping topics (controlled environments, root phenotyping and others) will be covered by the respective sessions and based on the received abstracts. Details, and the registration page will be open soon on www.appn.at<http://www.appn.at> Looking forward to receiving your abstracts and meeting you in June! Best regards, Gernot Bodner, Boris Rewald (local organizers) & APPN board [signature_1677033384]<http://www.appn.at/>

Feb. 27, 2019

Open position @VBCF Plants: Bioinformatician/Data Analyst (full-time)

by Jez,Jakub

Dear friends, We have opened a position for a Bioinformatician/Data Analyst to join our PlantS team and support the construction and validation of PHENOPlant and help us build our HT plant phenotyping data analysis pipelines. In between large-scale HT phenotyping projects, and within free capacities, the candidate is intended also to work on other projects for our users (non-strictly plant phenotyping related projects). Please help us (and maybe also yourself) to find an excellent candidate to support your research and spread the word: https://www.viennabiocenter.org/vbcf-jobs/ https://twitter.com/VBCF_PlantS/status/1098153265253023744 https://www.linkedin.com/feed/update/urn:li:activity:6504015287585771520 https://www.viennabiocenter.org/about/news/large-infrastructure-project-phe… Thank you very much. Best, Jakub [VBC Logo] Jakub Jeż Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77 090<tel:+43%20664%208084%2077%20090> 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>

Feb. 21, 2019

Re: [Plants-user] LED light survey results and planned measures

by Jez,Jakub

Dear Andreas, thanks you for your feedback. Nothing will be changed without informing you in advance and preliminary small-scale test! We will consider the smaller pots in our test, thanks. Best, Jakub On 21.02.19, 11:54, "plants-user on behalf of Andreas Bachmair" <plants-user-bounces(a)lists.vbcf.ac.at on behalf of andreas.bachmair(a)univie.ac.at> wrote: Dear Jakub, thanks for this informantive e-mail. We use higher light intensity (60% at MFPL toip floor), except for mutants in phototropic light receptors, where we have lower intensity. We did not observe more algal growth than before. Generally, I would prefer not to change the watering regime for this reason (we use chamber 21). A less frequent watering would practically prohibit use of smaller pots - it is already clear that pots smaller than the 7x7 cm size cause some water stress towards the end of the watering periods, as opposed to the larger pots that store more water which lasts till the next sub-irrigation. So I am asking not to change watering in chamber 21, or if this is necessary only to change one side (the internet will have the settings listed, so that every user can choose). Sincerely, Andreas > On 21.02.2019, at 11:33, Jez,Jakub <jakub.jez(a)vbcf.ac.at> wrote: > > Dear all, > > I would like to inform you about the results of the LED light survey and the planned measures. > > We got in total only 18 forms back (11 GMI, 7 MFPL) which corresponds to around 14% of total facility users. > However, negative and positive feedback was reported; let us focus on the negative topics. > > Two main issues have been identified in common: > • Too wet soil conditions and thus heavy algae growth on the soil surface > • Stressed plants (anthocyanins formation, early flowering, etc.) > > Add. 1: > The phytotrons and the light quality were designed and optimized towards providing best plant growth conditions; this applies unfortunately also to algae. > We assume that the lack of heat radiation, by using LED light, does not dry the soil surface in the same manner like fluorescent tubes did in the past. > In the next weeks we will test measures that could be applied towards optimal watering conditions. This will include an adjustment in the watering regime from twice a week to once in 5 days and adjustments in the watering holding time. It will be a challenge to find a compromise facilitating best watering conditions for young and older plants; Arabidopsis and e.g. N. benthamiana or others. > In parallel we will test different soil/sand/perlite ratios to optimize (lower) the water-holding abilities of the substrate. In case you have any suggestions/experience please do not hesitate to contact us. > We also suggest to not use the tray lids for young plants; or at least to reduce the time from one week to 2-3 days. > > Add. 2.: > Here we assume that the plant stress is caused by a too high light intensity; especially by the portion of the blue spectral range. (The wet soil (1.) might also contribute the total stress reaction). > In short, the new data and calculations indicates that the originally set values of 42% (GMI) and 46% (MFPL) were most probably too high for some of your accessions/mutants/lines. > At least they are too high to be considered as an overall standard setting. > The measured total intensity (µMol*m-2*-1) of the LED light is NOT equal to the same total intensity value of fluorescent tubes. This is mainly caused by the fact of the two different light qualities and the resulting different distribution of individual photons over the spectral range. > Our detailed spectral measurements suggest using a setting of 32% (GMI) and 38% (MFPL) as standard; especially in case of sensitive lines and/or experiments. > This settings will give you the same amount of photons belonging to the blue- and red spectral range as by using 4 fluorescent tubes. > All of you who are already happy with using higher values (60% and even 100%) can of course keep this settings. On the other hand, also lower settings might be meaningful in some cases. > We will also prepare a table/graph showing the relation of the set value to the total measured intensity. > > Please feel free to test the suggested settings in your phytotron/shelves. > How to: press both buttons at the same time until the value starts flashing, set then the desired value by pressing plus or minus button. Wait until the new setting stops flashing. > Alternatively you can also ask the facility staff to change the settings for you. > > We will ask you for your feedback on this new settings in the near future. > > In case of any comments or questions please do not hesitate to contact us. > > Best, Jakub > > P.S.: The different settings for GMI and MFPL phytotrons results from the different distance between your plants and the light source. > > > Jakub Jeż > Head, Plant Sciences Facility > T +43 1 7962324 7090 > M +43 664 8084 77 090 > jakub.jez(a)vbcf.ac.at > Vienna BioCenter Core Facilities GmbH > Dr. Bohr-Gasse 3 > 1030 Vienna > Austria > www.vbcf.ac.at > > > > > > > > > _______________________________________________ > plants-user mailing list > plants-user(a)lists.vbcf.ac.at > https://www.vbcf.ac.at/mailman/listinfo/plants-user _______________________________________________ plants-user mailing list plants-user(a)lists.vbcf.ac.at https://www.vbcf.ac.at/mailman/listinfo/plants-user

Feb. 21, 2019

Re: [Plants-user] LED light survey results and planned measures

by Andreas Bachmair

Dear Jakub, thanks for this informantive e-mail. We use higher light intensity (60% at MFPL toip floor), except for mutants in phototropic light receptors, where we have lower intensity. We did not observe more algal growth than before. Generally, I would prefer not to change the watering regime for this reason (we use chamber 21). A less frequent watering would practically prohibit use of smaller pots - it is already clear that pots smaller than the 7x7 cm size cause some water stress towards the end of the watering periods, as opposed to the larger pots that store more water which lasts till the next sub-irrigation. So I am asking not to change watering in chamber 21, or if this is necessary only to change one side (the internet will have the settings listed, so that every user can choose). Sincerely, Andreas > On 21.02.2019, at 11:33, Jez,Jakub <jakub.jez(a)vbcf.ac.at> wrote: > > Dear all, > > I would like to inform you about the results of the LED light survey and the planned measures. > > We got in total only 18 forms back (11 GMI, 7 MFPL) which corresponds to around 14% of total facility users. > However, negative and positive feedback was reported; let us focus on the negative topics. > > Two main issues have been identified in common: > • Too wet soil conditions and thus heavy algae growth on the soil surface > • Stressed plants (anthocyanins formation, early flowering, etc.) > > Add. 1: > The phytotrons and the light quality were designed and optimized towards providing best plant growth conditions; this applies unfortunately also to algae. > We assume that the lack of heat radiation, by using LED light, does not dry the soil surface in the same manner like fluorescent tubes did in the past. > In the next weeks we will test measures that could be applied towards optimal watering conditions. This will include an adjustment in the watering regime from twice a week to once in 5 days and adjustments in the watering holding time. It will be a challenge to find a compromise facilitating best watering conditions for young and older plants; Arabidopsis and e.g. N. benthamiana or others. > In parallel we will test different soil/sand/perlite ratios to optimize (lower) the water-holding abilities of the substrate. In case you have any suggestions/experience please do not hesitate to contact us. > We also suggest to not use the tray lids for young plants; or at least to reduce the time from one week to 2-3 days. > > Add. 2.: > Here we assume that the plant stress is caused by a too high light intensity; especially by the portion of the blue spectral range. (The wet soil (1.) might also contribute the total stress reaction). > In short, the new data and calculations indicates that the originally set values of 42% (GMI) and 46% (MFPL) were most probably too high for some of your accessions/mutants/lines. > At least they are too high to be considered as an overall standard setting. > The measured total intensity (µMol*m-2*-1) of the LED light is NOT equal to the same total intensity value of fluorescent tubes. This is mainly caused by the fact of the two different light qualities and the resulting different distribution of individual photons over the spectral range. > Our detailed spectral measurements suggest using a setting of 32% (GMI) and 38% (MFPL) as standard; especially in case of sensitive lines and/or experiments. > This settings will give you the same amount of photons belonging to the blue- and red spectral range as by using 4 fluorescent tubes. > All of you who are already happy with using higher values (60% and even 100%) can of course keep this settings. On the other hand, also lower settings might be meaningful in some cases. > We will also prepare a table/graph showing the relation of the set value to the total measured intensity. > > Please feel free to test the suggested settings in your phytotron/shelves. > How to: press both buttons at the same time until the value starts flashing, set then the desired value by pressing plus or minus button. Wait until the new setting stops flashing. > Alternatively you can also ask the facility staff to change the settings for you. > > We will ask you for your feedback on this new settings in the near future. > > In case of any comments or questions please do not hesitate to contact us. > > Best, Jakub > > P.S.: The different settings for GMI and MFPL phytotrons results from the different distance between your plants and the light source. > > > Jakub Jeż > Head, Plant Sciences Facility > T +43 1 7962324 7090 > M +43 664 8084 77 090 > jakub.jez(a)vbcf.ac.at > Vienna BioCenter Core Facilities GmbH > Dr. Bohr-Gasse 3 > 1030 Vienna > Austria > www.vbcf.ac.at > > > > > > > > > _______________________________________________ > plants-user mailing list > plants-user(a)lists.vbcf.ac.at > https://www.vbcf.ac.at/mailman/listinfo/plants-user

Feb. 21, 2019

LED light survey results and planned measures

by Jez,Jakub

Dear all, I would like to inform you about the results of the LED light survey and the planned measures. We got in total only 18 forms back (11 GMI, 7 MFPL) which corresponds to around 14% of total facility users. However, negative and positive feedback was reported; let us focus on the negative topics. Two main issues have been identified in common: 1. Too wet soil conditions and thus heavy algae growth on the soil surface 2. Stressed plants (anthocyanins formation, early flowering, etc.) Add. 1: The phytotrons and the light quality were designed and optimized towards providing best plant growth conditions; this applies unfortunately also to algae. We assume that the lack of heat radiation, by using LED light, does not dry the soil surface in the same manner like fluorescent tubes did in the past. In the next weeks we will test measures that could be applied towards optimal watering conditions. This will include an adjustment in the watering regime from twice a week to once in 5 days and adjustments in the watering holding time. It will be a challenge to find a compromise facilitating best watering conditions for young and older plants; Arabidopsis and e.g. N. benthamiana or others. In parallel we will test different soil/sand/perlite ratios to optimize (lower) the water-holding abilities of the substrate. In case you have any suggestions/experience please do not hesitate to contact us. We also suggest to not use the tray lids for young plants; or at least to reduce the time from one week to 2-3 days. Add. 2.: Here we assume that the plant stress is caused by a too high light intensity; especially by the portion of the blue spectral range. (The wet soil (1.) might also contribute the total stress reaction). In short, the new data and calculations indicates that the originally set values of 42% (GMI) and 46% (MFPL) were most probably too high for some of your accessions/mutants/lines. At least they are too high to be considered as an overall standard setting. The measured total intensity (µMol*m-2*-1) of the LED light is NOT equal to the same total intensity value of fluorescent tubes. This is mainly caused by the fact of the two different light qualities and the resulting different distribution of individual photons over the spectral range. Our detailed spectral measurements suggest using a setting of 32% (GMI) and 38% (MFPL) as standard; especially in case of sensitive lines and/or experiments. This settings will give you the same amount of photons belonging to the blue- and red spectral range as by using 4 fluorescent tubes. All of you who are already happy with using higher values (60% and even 100%) can of course keep this settings. On the other hand, also lower settings might be meaningful in some cases. We will also prepare a table/graph showing the relation of the set value to the total measured intensity. Please feel free to test the suggested settings in your phytotron/shelves. How to: press both buttons at the same time until the value starts flashing, set then the desired value by pressing plus or minus button. Wait until the new setting stops flashing. Alternatively you can also ask the facility staff to change the settings for you. We will ask you for your feedback on this new settings in the near future. In case of any comments or questions please do not hesitate to contact us. Best, Jakub P.S.: The different settings for GMI and MFPL phytotrons results from the different distance between your plants and the light source. [VBC Logo] Jakub Jeż Head, Plant Sciences Facility T +43 1 7962324 7090<tel:+43179623247090> M +43 664 8084 77 090<tel:+43%20664%208084%2077%20090> 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>

Feb. 21, 2019