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Moritz Negwer<p>In case anyone was following the recent Science paper about using Tartrazine for <a href="https://mstdn.science/tags/tissueclearing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>tissueclearing</span></a>, apparently there is at least one (competing) group that couldn't reproduce it and wrote a preprint about it: </p><p>Tartrazine cannot make live tissues transparent<br><a href="https://doi.org/10.1101/2024.09.29.615648" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.1101/2024.09.29.615</span><span class="invisible">648</span></a> </p><p>Discussion on Pubpeer, including the Tartrazine paper's author's response: <br><a href="https://pubpeer.com/publications/81314BB3706B3D6ADAD49F301B2FA5" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">pubpeer.com/publications/81314</span><span class="invisible">BB3706B3D6ADAD49F301B2FA5</span></a></p><p><a href="https://mstdn.science/tags/lightsheet" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>lightsheet</span></a> <a href="https://mstdn.science/tags/microscopy" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>microscopy</span></a> <a href="https://mstdn.science/tags/tartrazine" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>tartrazine</span></a></p>
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#tissueclearing
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Moritz Negwer<p>Very excited that our whole-mouse-brain analysis pipeline - DELiVR - is published now at Nature Methods. With DELiVR, we built an open-source, easy-to-use pipeline for analyzing image stacks from cleared mouse brains. </p><p>Paper: <a href="https://www.nature.com/articles/s41592-024-02245-2" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">nature.com/articles/s41592-024</span><span class="invisible">-02245-2</span></a> <br>Code: <a href="https://github.com/erturklab/delivr_cfos" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/erturklab/delivr_cf</span><span class="invisible">os</span></a><br>Docker containers, test dataset, handbook: <a href="https://www.discotechnologies.org/DELiVR/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="">discotechnologies.org/DELiVR/</span><span class="invisible"></span></a></p><p><a href="https://mstdn.science/tags/neuroscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>neuroscience</span></a> <a href="https://mstdn.science/tags/tissueclearing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>tissueclearing</span></a> <a href="https://mstdn.science/tags/lightsheet" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>lightsheet</span></a> <a href="https://mstdn.science/tags/imageanalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>imageanalysis</span></a></p>
Moritz Negwer<p>Check out our lab's <a href="https://mstdn.science/tags/newpaper" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>newpaper</span></a> in <span class="h-card"><a href="https://mstdn.science/@cellpress" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>cellpress</span></a></span> Cell: <br>We found that the skull is special - its marrow is a special immunologic niche. Skull <a href="https://mstdn.science/tags/Immune" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Immune</span></a> <a href="https://mstdn.science/tags/cells" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cells</span></a> can move to the meninges via skull-meninges connections, which we found both in mice and humans with <a href="https://mstdn.science/tags/tissueclearing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>tissueclearing</span></a> and <a href="https://mstdn.science/tags/lightsheet" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>lightsheet</span></a> <a href="https://mstdn.science/tags/microscopy" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>microscopy</span></a>. <br>We also bring <a href="https://mstdn.science/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> and <a href="https://mstdn.science/tags/PETimaging" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PETimaging</span></a> to the mix! </p><p>Paper: <a href="https://doi.org/10.1016/j.cell.2023.07.009" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.1016/j.cell.2023.07</span><span class="invisible">.009</span></a></p><p>Explainer thread:<br><a href="https://bird.makeup/users/erturklab/statuses/1689293936185991169" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">bird.makeup/users/erturklab/st</span><span class="invisible">atuses/1689293936185991169</span></a></p>
Moritz Negwer<p>Preprint alert! Our lab developed targetable <a href="https://mstdn.science/tags/DNA" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>DNA</span></a> origami <a href="https://mstdn.science/tags/nanoparticles" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>nanoparticles</span></a>, which we then image throughout the entire (transparent) mouse body using <a href="https://mstdn.science/tags/lightsheet" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>lightsheet</span></a> <a href="https://mstdn.science/tags/microscopy" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>microscopy</span></a>. </p><p>Our DNA origami were able to target immune cells, as well as a subset of cancer metastases in the lung. </p><p>Preprint:<br><a href="https://www.biorxiv.org/content/10.1101/2023.07.24.550304v1.full.pdf" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">23.07.24.550304v1.full.pdf</span></a></p><p>Explainer thread: <br><a href="https://bird.makeup/users/erturklab/statuses/1686331791022448640" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">bird.makeup/users/erturklab/st</span><span class="invisible">atuses/1686331791022448640</span></a></p><p><a href="https://mstdn.science/tags/preprint" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>preprint</span></a> <a href="https://mstdn.science/tags/tissueclearing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>tissueclearing</span></a></p>
Haojia Wu<p>More and more spatial proteomics techniques are out! This time DISCO-MS! Aided by AI and robotics, DISCO-MS generates proteome data indistinguishable from fresh samples. <a href="https://mastodon.haojia-wu.com/tags/proteomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>proteomics</span></a> <a href="https://mastodon.haojia-wu.com/tags/tissueclearing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>tissueclearing</span></a> <a href="https://mastodon.haojia-wu.com/tags/deeplearning" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>deeplearning</span></a> <br><a href="https://www.cell.com/cell/fulltext/S0092-8674(22)01465-9" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">cell.com/cell/fulltext/S0092-8</span><span class="invisible">674(22)01465-9</span></a></p>
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