[3dem] 3dem Digest, Vol 151, Issue 6

Kolivand, Hoshang H.Kolivand at ljmu.ac.uk
Mon Mar 9 00:57:57 PDT 2020 

Hi,
Could someone please let me know what this group email is about and why I have been added?
Hoshang
From: 3dem <3dem-bounces at ncmir.ucsd.edu> On Behalf Of Benjamin Himes
Sent: 07 March 2020 00:17
To: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] 3dem Digest, Vol 151, Issue 6

I'd like to echo Steve's question....i'm a co-author on last year's paper, and haven't been able to read it. Really questioning the eurographics model..

Nice idea, but the suppression of info is a prob.

Ben H.

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Today's Topics:

   1. SHape REtrieval Contest (SHREC) 2020 track "Classification in
      Cryo-Electron Tomograms" (Friedrich F?rster)
   2. Re: SHape REtrieval Contest (SHREC) 2020 track
      "Classification in Cryo-Electron Tomograms" (Ludtke, Steven J.)


----------------------------------------------------------------------

Message: 1
Date: Thu, 5 Mar 2020 21:32:58 +0100
From: Friedrich F?rster <f.g.forster at uu.nl<mailto:f.g.forster at uu.nl>>
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Subject: [3dem] SHape REtrieval Contest (SHREC) 2020 track
        "Classification in Cryo-Electron Tomograms"
Message-ID:
        <CALtyCEivD7bbBX8d7+-ag7CMvPFyxVW5cDL7tJrr5h+1sRobDg at mail.gmail.com<mailto:CALtyCEivD7bbBX8d7%2B-ag7CMvPFyxVW5cDL7tJrr5h%2B1sRobDg at mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"

Dear 3D-EM,



We would like to announce SHape REtrieval Contest (SHREC) 2020 track
"Classification in Cryo-Electron Tomograms". In this track, we propose a
task of localization and classification of biological particles in the
cryo-electron tomograms. We provide a dataset of simulated tomograms with
annotations and additional ground truth information. We hope this will
enable researchers to try out different methods, including machine learning
approaches.



Track participants will have 4 weeks to send us their results (text file
with a list of found and classified particles, and one-page description of
their method). Track results are evaluated, analyzed and combined into a
joint paper, that will be submitted to and presented at 3D Object Retrieval
Workshop, 4-5 September 2020: https://workshop.cgv.tugraz.at/3dor2020/<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fworkshop.cgv.tugraz.at%2f3dor2020%2f&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-6295b3f8421ea8bbf185a5861b6d5f19c0e2a5de>

The general objective of the SHREC is to evaluate the effectiveness and
compare localization and classification methods.



If you are interested, please check out the website for more information:
http://www.shrec.net/cryo-et/<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.shrec.net%2fcryo%2det%2f&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-269f345cada718f0d3f7af919f2ea86711e0641c>



Best regards



Ilja Gubins, Gijs van der Schot, Marten Chaillet, Remco Veltkamp, Friedrich
F?rster

--
prof. dr. Friedrich Foerster

Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands

Tel: +31 30 253 4318

http://www.uu.nl/en/research/cryo-em<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.uu.nl%2fen%2fresearch%2fcryo%2dem&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-8828f786041c962913d87047939d019f5e89707d>
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------------------------------

Message: 2
Date: Thu, 5 Mar 2020 22:07:00 +0000
From: "Ludtke, Steven J." <sludtke at bcm.edu<mailto:sludtke at bcm.edu>>
To: Friedrich F?rster <f.g.forster at uu.nl<mailto:f.g.forster at uu.nl>>
Cc: "3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Re: [3dem] SHape REtrieval Contest (SHREC) 2020 track
        "Classification in Cryo-Electron Tomograms"
Message-ID: <2DA60190-8015-4883-8565-A96DDA1E7E05 at bcm.edu<mailto:2DA60190-8015-4883-8565-A96DDA1E7E05 at bcm.edu>>
Content-Type: text/plain; charset="utf-8"

Hi Fredrich,
were the results from the last one ever made publicly available? Is the data and/or results of the last one available online somewhere?  I looked briefly, and could find websites mentioning it, but little else?   Not much motivation to participate if the results are all closed (other than resulting publications, of course).

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <sludtke at bcm.edu<mailto:sludtke at bcm.edu><mailto:sludtke at bcm.edu<mailto:sludtke at bcm.edu>>>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.bcm.edu%2fbiochem&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-809c25d7496f4ac0cb53a1f93cb1aa7574fec342><http://www.bcm.edu/biochem<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.bcm.edu%2fbiochem&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-809c25d7496f4ac0cb53a1f93cb1aa7574fec342>>)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fcryoem.bcm.edu&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-484c59cac388c33d833c3a7d8fb6697fb0137bdb><http://cryoem.bcm.edu<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fcryoem.bcm.edu&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-484c59cac388c33d833c3a7d8fb6697fb0137bdb>>)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.bcm.edu%2fresearch%2fcibr&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-941a38728d7ca597c0894ceed59145a6486d6ecc><http://www.bcm.edu/research/cibr<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.bcm.edu%2fresearch%2fcibr&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-941a38728d7ca597c0894ceed59145a6486d6ecc>>)



On Mar 5, 2020, at 2:32 PM, Friedrich F?rster <f.g.forster at uu.nl<mailto:f.g.forster at uu.nl><mailto:f.g.forster at uu.nl<mailto:f.g.forster at uu.nl>>> wrote:

***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.
________________________________
Dear 3D-EM,

We would like to announce SHape REtrieval Contest (SHREC) 2020 track "Classification in Cryo-Electron Tomograms". In this track, we propose a task of localization and classification of biological particles in the cryo-electron tomograms. We provide a dataset of simulated tomograms with annotations and additional ground truth information. We hope this will enable researchers to try out different methods, including machine learning approaches.

Track participants will have 4 weeks to send us their results (text file with a list of found and classified particles, and one-page description of their method). Track results are evaluated, analyzed and combined into a joint paper, that will be submitted to and presented at 3D Object Retrieval Workshop, 4-5 September 2020: https://workshop.cgv.tugraz.at/3dor2020/<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fworkshop.cgv.tugraz.at%2f3dor2020%2f&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-6295b3f8421ea8bbf185a5861b6d5f19c0e2a5de><https://urldefense.proofpoint.com/v2/url?u=https-3A__workshop.cgv.tugraz.at_3dor2020_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=WQWsg1ffsdRMpCT3N2KurlValKUv0BSA79S5TEtJwJI&s=ZRhUa-_ujY1hScNGihjC3eox3CQMLTVVLJNwpVIO8No&e=<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2furldefense.proofpoint.com%2fv2%2furl%3fu%3dhttps%2d3A%5f%5fworkshop.cgv.tugraz.at%5f3dor2020%5f%26d%3dDwMFaQ%26c%3dZQs%2dKZ8oxEw0p81sqgiaRA%26r%3dDk5VoQQ%2dwINYVssLMZihyC5Dj%5fsWYKxCyKz9E4Lp3gc%26m%3dWQWsg1ffsdRMpCT3N2KurlValKUv0BSA79S5TEtJwJI%26s%3dZRhUa%2d%5fujY1hScNGihjC3eox3CQMLTVVLJNwpVIO8No%26e%3d&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-46129339df5efd0b6f8af0995c15c94a6cdb4b64>>
The general objective of the SHREC is to evaluate the effectiveness and compare localization and classification methods.

If you are interested, please check out the website for more information: http://www.shrec.net/cryo-et/<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.shrec.net%2fcryo%2det%2f&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-269f345cada718f0d3f7af919f2ea86711e0641c><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.shrec.net_cryo-2Det_&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=WQWsg1ffsdRMpCT3N2KurlValKUv0BSA79S5TEtJwJI&s=Na6EdCP08UsaaLiGVvgtlDpGfo_I_7UqfTLhyFVjTpY&e=<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2furldefense.proofpoint.com%2fv2%2furl%3fu%3dhttp%2d3A%5f%5fwww.shrec.net%5fcryo%2d2Det%5f%26d%3dDwMFaQ%26c%3dZQs%2dKZ8oxEw0p81sqgiaRA%26r%3dDk5VoQQ%2dwINYVssLMZihyC5Dj%5fsWYKxCyKz9E4Lp3gc%26m%3dWQWsg1ffsdRMpCT3N2KurlValKUv0BSA79S5TEtJwJI%26s%3dNa6EdCP08UsaaLiGVvgtlDpGfo%5fI%5f7UqfTLhyFVjTpY%26e%3d&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-7871df49ba8bb2bb9e99f228de9bdfebfdc37574>>

Best regards

Ilja Gubins, Gijs van der Schot, Marten Chaillet, Remco Veltkamp, Friedrich F?rster

--
prof. dr. Friedrich Foerster

Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands

Tel: +31 30 253 4318

http://www.uu.nl/en/research/cryo-em<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fwww.uu.nl%2fen%2fresearch%2fcryo%2dem&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-8828f786041c962913d87047939d019f5e89707d><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uu.nl_en_research_cryo-2Dem&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=WQWsg1ffsdRMpCT3N2KurlValKUv0BSA79S5TEtJwJI&s=AzonDRX9DtQIG5Ieb7z1Fm4BfNFNs1S76l_r2Sd6sKM&e=<https://hes32-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2furldefense.proofpoint.com%2fv2%2furl%3fu%3dhttp%2d3A%5f%5fwww.uu.nl%5fen%5fresearch%5fcryo%2d2Dem%26d%3dDwMFaQ%26c%3dZQs%2dKZ8oxEw0p81sqgiaRA%26r%3dDk5VoQQ%2dwINYVssLMZihyC5Dj%5fsWYKxCyKz9E4Lp3gc%26m%3dWQWsg1ffsdRMpCT3N2KurlValKUv0BSA79S5TEtJwJI%26s%3dAzonDRX9DtQIG5Ieb7z1Fm4BfNFNs1S76l%5fr2Sd6sKM%26e%3d&umid=18d1ada8-52a8-4c35-9183-af83326ab9b5&auth=768f192bba830b801fed4f40fb360f4d1374fa7c-4ba175032d8c20be2073cfb4a1e033bc733fc797>>
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