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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Slack Export - #general</title>
<link rel=stylesheet type=text/css
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</head>
<body>
<div id="slack-archive-viewer">
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<h3 id="channel-title">Public Channels</h3>
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# careers
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# clearing
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# commercial
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# lattice
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# lavision-ultramicroscope
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# luxendo_muvi
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# meetings
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# protocols
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# publications
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# random
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# sampleprep
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# spim-commercial
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# zeiss_lightsheet
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<div id="2020-11-23 16:21:07">
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<div class="username">Neil Anthony
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<a href="#2020-11-23 16:21:07"><div class="time">2020-11-23 16:21:07</div></a>
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<p>@Neil Anthony has joined the channel</p>
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<div id="2020-12-04 23:57:33">
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<div class="username">Gaurav Joshi
<span class="print-only user-email">([email protected])</span>
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<a href="#2020-12-04 23:57:33"><div class="time">2020-12-04 23:57:33</div></a>
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<p>@Gaurav Joshi has joined the channel</p>
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<div id="2020-12-06 14:35:14">
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<div class="username">Cesar Augusto VALADES-CRUZ
<span class="print-only user-email">([email protected])</span>
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<a href="#2020-12-06 14:35:14"><div class="time">2020-12-06 14:35:14</div></a>
<div class="msg">
<p>@Cesar Augusto VALADES-CRUZ has joined the channel</p>
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<div class="message-container channel_join ">
<div id="2020-12-07 16:11:59">
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<div class="username">Alessandro Ciccarelli
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-07 16:11:59"><div class="time">2020-12-07 16:11:59</div></a>
<div class="msg">
<p>@Alessandro Ciccarelli has joined the channel</p>
</div>
</div>
</div>
</div>
<div class="message-container channel_join ">
<div id="2020-12-08 12:36:50">
<img src="https://avatars.slack-edge.com/2020-12-10/1557871841974_a05a27bf7ce833e05a41_72.jpg" class="user_icon" />
<div class="message">
<div class="username">Dee Kavanagh
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-08 12:36:50"><div class="time">2020-12-08 12:36:50</div></a>
<div class="msg">
<p>@Dee Kavanagh has joined the channel</p>
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<div id="2020-12-09 12:45:17">
<img src="https://avatars.slack-edge.com/2020-12-09/1567510911348_d6aed3d2c44f9bdc9863_72.jpg" class="user_icon" />
<div class="message">
<div class="username">Alessandro Ciccarelli
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-09 12:45:17"><div class="time">2020-12-09 12:45:17</div></a>
<div class="msg">
<p>Hey, Hi! Thanks Neil for setting this up!</p>
</div>
</div>
</div>
</div>
<div class="message-container">
<div id="2020-12-09 19:11:02">
<img src="https://avatars.slack-edge.com/2020-12-04/1551870045442_c73f6ea460860df42e2a_72.jpg" class="user_icon" />
<div class="message">
<div class="username">Neil Anthony
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-09 19:11:02"><div class="time">2020-12-09 19:11:02</div></a>
<div class="msg">
<p>Hi @Alessandro Ciccarelli, my pleasure. Excited to be part of the light sheet group.</p>
</div>
</div>
</div>
</div>
<div class="message-container">
<div id="2020-12-10 12:05:24">
<img src="https://avatars.slack-edge.com/2020-12-10/1557871841974_a05a27bf7ce833e05a41_72.jpg" class="user_icon" />
<div class="message">
<div class="username">Dee Kavanagh
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-10 12:05:24"><div class="time">2020-12-10 12:05:24</div></a>
<div class="msg">
<p>Yes, thanks again Neil! I think I am going to enjoy using slack! I can think of all sorts to do with it now in work</p>
</div>
</div>
</div>
</div>
<div class="message-container channel_join ">
<div id="2020-12-16 09:05:20">
<img src="https://avatars.slack-edge.com/2021-12-20/2856115809958_6b7a9699027b862074a8_72.jpg" class="user_icon" />
<div class="message">
<div class="username">Helena Coker
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-16 09:05:20"><div class="time">2020-12-16 09:05:20</div></a>
<div class="msg">
<p>@Helena Coker has joined the channel</p>
</div>
</div>
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<div class="message-container">
<div id="2020-12-17 11:09:42">
<img src="https://avatars.slack-edge.com/2020-12-09/1567510911348_d6aed3d2c44f9bdc9863_72.jpg" class="user_icon" />
<div class="message">
<div class="username">Alessandro Ciccarelli
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-17 11:09:42"><div class="time">2020-12-17 11:09:42</div></a>
<div class="msg">
<p>My question of the week: I ve beeen playing a bit with deconvolution (Huygens) for light-sheet data (from MuVi spim and Lavision UMII); I then realized that both have lenses and pixels giving downsampling and making deconvolution quite inefficient; I then realized that just with a " background substraction" I can get very nice results(See picture)! Do you see any big drwabacks/hiddedn dangers in using this basic filtering? And if you have positive experience with light-sheet-deconvolution, maybe we can one day doscsuss about it..</p>
<div class="message-upload">
<div class="link-title"><a href="None"></a></div>
<!-- no preview available -->
</div>
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<div id="2020-12-18 12:44:02">
<img src="https://avatars.slack-edge.com/2021-12-20/2856115809958_6b7a9699027b862074a8_72.jpg" class="user_icon_reply" />
<div class="reply">
<div class="username">Helena Coker
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-18 12:44:02"><div class="time">2020-12-18 12:44:02</div></a>
<div class="msg">
<p><strong><em>*Thread Reply:</em>*</strong> This is a great example and why we need to get analysis people in this group ASAP!</p>
<p>from my limited experience, and what I've gleaned from Claire and Laura in CAMDU, it very much depends what your aim is from the processed data. If it's just a pretty picture then you're okay but tracking/segmentation you might want to be a bit more careful and from FIJIs guidance on that plugin: "As a rule of thumb, for 8-bit or RGB images it should be at least as large as the radius of the largest object in the image that is not part of the background."
If you want to do something quantitative then it's another ball game.</p>
</div>
</div>
</div>
</div>
<div class="message-container">
<div id="2020-12-21 15:49:59">
<img src="https://avatars.slack-edge.com/2020-12-09/1567510911348_d6aed3d2c44f9bdc9863_72.jpg" class="user_icon_reply" />
<div class="reply">
<div class="username">Alessandro Ciccarelli
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-21 15:49:59"><div class="time">2020-12-21 15:49:59</div></a>
<div class="msg">
<p><strong><em>*Thread Reply:</em>*</strong> Thanks fror the feedback! I agree and I read the FIJI descrption; and the the value I was using it was actually not the one reccomended..But the image looked, accordingly to my imaging/bilogical experince, more similar to the "ground truth"; yes, some analysis people are always welcome!</p>
</div>
</div>
</div>
</div>
<div class="message-container">
<div id="2020-12-21 15:55:38">
<img src="https://avatars.slack-edge.com/2020-12-09/1567510911348_d6aed3d2c44f9bdc9863_72.jpg" class="user_icon_reply" />
<div class="reply">
<div class="username">Alessandro Ciccarelli
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2020-12-21 15:55:38"><div class="time">2020-12-21 15:55:38</div></a>
<div class="msg">
<p><strong><em>*Thread Reply:</em>*</strong> And other point for future discussion: il light-sheet really good for quantitative analysis?..In the sample I image (cleared and not ) I see a lot of artefcats due to side illuminations, Gaussian shape of the beams, not good clearing,.I m also wondering what is the space/utility in science for "not-quantitative" analyses..</p>
</div>
</div>
</div>
</div>
<div class="message-container channel_join ">
<div id="2021-01-05 18:21:40">
<img src="https://secure.gravatar.com/avatar/864cc411cdde7d3514da4ed12f44fbf0.jpg?s=72&d=https%3A%2F%2Fa.slack-edge.com%2Fdf10d%2Fimg%2Favatars%2Fava_0023-72.png" class="user_icon" />
<div class="message">
<div class="username">Jenny Schafer
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2021-01-05 18:21:40"><div class="time">2021-01-05 18:21:40</div></a>
<div class="msg">
<p>@Jenny Schafer has joined the channel</p>
</div>
</div>
</div>
</div>
<div class="message-container">
<div id="2021-01-05 18:29:04">
<img src="https://secure.gravatar.com/avatar/864cc411cdde7d3514da4ed12f44fbf0.jpg?s=72&d=https%3A%2F%2Fa.slack-edge.com%2Fdf10d%2Fimg%2Favatars%2Fava_0023-72.png" class="user_icon" />
<div class="message">
<div class="username">Jenny Schafer
<span class="print-only user-email">([email protected])</span>
</div>
<a href="#2021-01-05 18:29:04"><div class="time">2021-01-05 18:29:04</div></a>
<div class="msg">
<p>Hi, everyone! My name is Jenny Schafer, and I am Managing Director of the Cell Imaging Shared Resource (CISR) at Vanderbilt University in Nashville, TN, USA. Neil Anthony just invited our group to join. We have a Zeiss Z.1 as well as two custom built lightsheet systems -- Lattice Lightsheet and Scanned Oblique Planed Illumination (SOPi). All have been installed in our core in 2020, so we are still learning a lot. Also, hello to Alessandro! Kurt Anderson suggested I get in touch with you as well, so I'm glad to see you here.</p>
</div>
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<div class="message-container">
<div id="2021-01-06 08:47:09">
<img src="https://avatars.slack-edge.com/2021-12-20/2856115809958_6b7a9699027b862074a8_72.jpg" class="user_icon_reply" />
<div class="reply">
<div class="username">Helena Coker
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 08:47:09"><div class="time">2021-01-06 08:47:09</div></a>
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<p><strong><em>*Thread Reply:</em>*</strong> Hi Jenny, I really enjoyed your talk yesterday and I'm glad you're here! as you can see we're a select bunch in the early stages at the moment but hoping it will grow into a useful monster.</p>
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<div id="2021-01-06 09:46:46">
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<div class="username">Alessandro Ciccarelli
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 09:46:46"><div class="time">2021-01-06 09:46:46</div></a>
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<p><strong><em>*Thread Reply:</em>*</strong> Hi Jenny, nice to meet you! I was actually thinkin to write to you today! I also liked your talk and I found interesting the idea of the assisted/pilot test for new users (something I m also basically forced to do everytime..). Woudl you like maybe to have a zoom chat next week, where we can share ideas about light-sheet outreach& training? Maybe we can also invite the colleagues of this nice new "slack lightsheet comunity" (we are max 8 people..)? Otherwise I ll write you an e-mail</p>
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<div id="2021-01-06 19:02:45">
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<div class="username">Jenny Schafer
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 19:02:45"><div class="time">2021-01-06 19:02:45</div></a>
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<p><strong><em>*Thread Reply:</em>*</strong> Thanks, @Helena Coker! And thanks for getting this group started. @Alessandro Ciccarelli, I just sent you a message here.</p>
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<div class="username">Georgina Fletcher
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 13:22:22"><div class="time">2021-01-06 13:22:22</div></a>
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<p>@Georgina Fletcher has joined the channel</p>
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<div id="2021-01-06 13:27:25">
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<div class="username">Georgina Fletcher
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 13:27:25"><div class="time">2021-01-06 13:27:25</div></a>
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<p>Hi @here! Thanks to @Dee Kavanagh for the invite to join your slack channel! I'm the project officer for BioImagingUK, an open network for life scientists working with imaging technologies. I'm looking forward to helping out and growing the Lightsheet community with you.</p>
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🙌 Helena Coker, Dee Kavanagh
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<div id="2021-01-06 13:38:12">
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<div class="username">Alessandro Ciccarelli
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 13:38:12"><div class="time">2021-01-06 13:38:12</div></a>
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<p>Hi Gerorgina! Welcome on board!</p>
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👋 Georgina Fletcher
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<div id="2021-01-06 13:38:33">
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<div class="username">Dee Kavanagh
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 13:38:33"><div class="time">2021-01-06 13:38:33</div></a>
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<p>Thank you Georgina, welcome to our Slack 🙂 its great to have you here and to have the support of BioImaging UK!</p>
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👍 Georgina Fletcher
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<div id="2021-01-06 13:40:20">
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<div class="username">Neil Anthony
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 13:40:20"><div class="time">2021-01-06 13:40:20</div></a>
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<p>Hi @Georgina Fletcher, welcome to the group 🙂</p>
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👋 Georgina Fletcher
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<div class="username">Kevin Mackenzie
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<a href="#2021-01-06 16:50:58"><div class="time">2021-01-06 16:50:58</div></a>
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<p>@Kevin Mackenzie has joined the channel</p>
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<div class="username">Dave Johnston
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<a href="#2021-01-06 16:52:40"><div class="time">2021-01-06 16:52:40</div></a>
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<p>@Dave Johnston has joined the channel</p>
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<div class="username">Michael Zachariadis
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 16:53:08"><div class="time">2021-01-06 16:53:08</div></a>
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<p>@Michael Zachariadis has joined the channel</p>
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<div class="username">Martin Lenz
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<a href="#2021-01-06 16:56:59"><div class="time">2021-01-06 16:56:59</div></a>
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<p>@Martin Lenz has joined the channel</p>
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<div id="2021-01-06 16:58:25">
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<div class="username">Dave Johnston
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 16:58:25"><div class="time">2021-01-06 16:58:25</div></a>
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<p>Hi All, Dave Johnston from Southampton (Biomedical Imaging Unit, UoS and based at the General Hospital). We have a rarely used LaVision Ultramicroscope2. Only maybe 2 publications in maybe 6 years and only a handful of users. Mouse brain, archival human brain and (curveball coming up) - antarctic mudstars.</p>
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<div id="2021-01-07 16:12:10">
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<div class="username">Dee Kavanagh
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-07 16:12:10"><div class="time">2021-01-07 16:12:10</div></a>
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<p><strong><em>*Thread Reply:</em>*</strong> Hi Dave, nice to meet you. We had an Ultra2 installed in 2019. I am based at the University of Birmingham. I have to say I love it in terms of its ease of use compared to some of our other light-sheets (lattice and diSPIM) systems. When first installed it got great reception (we are also based next to hospital the QE) and we pretty much image</p>
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<div id="2021-01-07 16:13:49">
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<div class="username">Dee Kavanagh
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-07 16:13:49"><div class="time">2021-01-07 16:13:49</div></a>
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<p><strong><em>*Thread Reply:</em>*</strong> mouse bits. I wonder if you have ever tried any of the automated clearing instruments? Clearing is one of our bottlenecks and I am looking to try ease the sample prep for our users.</p>
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<div id="2021-01-07 16:14:53">
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<div class="username">Dee Kavanagh
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-07 16:14:53"><div class="time">2021-01-07 16:14:53</div></a>
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<p><strong><em>*Thread Reply:</em>*</strong> Also what on earth is an Antarctic mudstar?!😁</p>
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<div id="2021-01-06 16:58:53">
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<div class="username">Michael Zachariadis
<span class="print-only user-email">([email protected])</span>
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<a href="#2021-01-06 16:58:53"><div class="time">2021-01-06 16:58:53</div></a>
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<p>Hi all, and thanks @Neil Anthony for the link to join. I'm managing the BioImaging service at the University of Bath, and just before the first lockdown we had our Z.1 installed and not really had the opportunity to work with it. It is great to have a group to turn too when questions arise 🙂</p>
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