<div dir="ltr"><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">Hello Cryo</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-ET world</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">!</span></font><div><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><br></span></font></div><div><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">We are currently developing <b>MemBrain</b></span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><b>-seg</b></span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, our new deep learning</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-based </span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">membrane segmentation tool</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, and we would like to get your feedback</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">!  </span></font></div><div><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><br></span></div><div><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">So far, we trained a neural network on a dataset of diverse membrane </span><font face="gg sans, Noto Sans, Helvetica Neue, Helvetica, Arial, sans-serif" style="color:rgb(0,0,0)">architectures</font><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, and it predicts membrane segmentations quite well on our data:</span></div><div><font color="#000000" face="gg sans, Noto Sans, Helvetica Neue, Helvetica, Arial, sans-serif"><br></font><div><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"> </span></font><div><img src="cid:ii_ljn96zzj1" alt="image.png" width="864" height="269" style="margin-right:0px"><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><br></span></font></div><div><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><br></span></font></div><div><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">Now</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, we would like to test the network's generalizability on tomograms from around the TeamTomo-verse</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">.  We would highly appreciate if you could give MemBrain</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-seg a try on your data</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"> and let us know how it works for you</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">.  </span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">We aim to make using MemBrain</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-seg as effortless as possible</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">: with its user</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-friendly command line interface</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, you can segment your tomograms within minutes</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">.</span></font><div><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><br></span></font></div><div><img src="cid:ii_ljn96lco0" alt="image.png" style="margin-right:0px" width="898" height="57"><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"> </span></font></div><div><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><br></span></font></div><div><font color="#000000" style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">You can access MemBrain</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-seg on the </span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><b>#teamtomo Github repository</b></span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">: </span><a href="https://urldefense.com/v3/__https://github.com/teamtomo/membrain-seg__;!!Mih3wA!H5hsdNPpe5GAI-V-hmcDyqudo1Lc8qoeJ-6cy6VLxyyPCovRat0eKWRS909vXDWQDkfGHK-fyZNr81VLWNSNORI$" rel="noreferrer noopener" title="https://github.com/teamtomo/membrain-seg" role="button" style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px;word-break:break-word" target="_blank"><span style="margin:0px;padding:0px;border:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;outline:0px">https://github.com/teamtomo/membrain-seg</span></a></font><div><font color="#000000"><br></font></div><div><font color="#000000"><span style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">The package includes functionalities for segmenting your tomograms</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, some optional preprocessing steps</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, as well as tools for re</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">training the model with your own data to fine-tune the performance (</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">although MemBrain-seg is intended to function well "out-of-the-box" without retraining).  </span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">For all these functionalities</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, you can find more information in our documentation </span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">(</span><a href="https://urldefense.com/v3/__https://github.com/teamtomo/membrain-seg/blob/main/docs/index.md__;!!Mih3wA!H5hsdNPpe5GAI-V-hmcDyqudo1Lc8qoeJ-6cy6VLxyyPCovRat0eKWRS909vXDWQDkfGHK-fyZNr81VLFwwqzEo$" rel="noreferrer noopener" title="https://github.com/teamtomo/membrain-seg/blob/main/docs/index.md" role="button" style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px;word-break:break-word" target="_blank"><span style="margin:0px;padding:0px;border:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;outline:0px">https://github.com/teamtomo/membrain-seg/blob/main/docs/index.md</span></a><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">)</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, or even in our YouTube video series about creating new training patches from your tomograms </span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">(</span><a href="https://urldefense.com/v3/__https://www.youtube.com/playlist?list=PLV3O3yHyCjkXAi9MWgComzh6JuKcHUgNU__;!!Mih3wA!H5hsdNPpe5GAI-V-hmcDyqudo1Lc8qoeJ-6cy6VLxyyPCovRat0eKWRS909vXDWQDkfGHK-fyZNr81VLx29hkX4$" rel="noreferrer noopener" title="https://www.youtube.com/playlist?list=PLV3O3yHyCjkXAi9MWgComzh6JuKcHUgNU" role="button" style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px;word-break:break-word" target="_blank"><span style="margin:0px;padding:0px;border:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;outline:0px">https://www.youtube.com/playlist?list=PLV3O3yHyCjkXAi9MWgComzh6JuKcHUgNU</span></a><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">)</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">.</span></span></font></div><div><font color="#000000"><span style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><br></span></span></font></div><div><font color="#000000"><span style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">MemBrain</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-seg is still under early development</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"> and may not work perfectly on your data</span><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">.  </span></span></font><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">In this case</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, we recommend to extract more patches from your tomograms and include them in the training dataset</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">.  I</span><span style="font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;color:rgb(0,0,0)">n our preliminary testing, performance improves significantly after only correcting a few new patches.  </span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">We are eager to extend the MemBrain-seg training dataset to cover more and more different views of membranes from a variety of cells and tomo acquisition parameters.  </span></div><div><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><br></span></div><div><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">So please reach out to us if you would like to collaborate on extending MemBrain-seg dataset to help improve the general performance for everyone.  It is not necessary to share full tomograms, only the small corrected patches.  </span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">If you have any questions or trouble running MemBrain</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-seg</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">, please also let us know – we are happy to receive feedback and assist in getting MemBrain</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-seg running well for you</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">.  </span><span style="color:rgb(0,0,0);font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;margin:0px;padding:0px;border:0px;vertical-align:baseline;outline:0px">We're looking forward to hearing about your experiences</span><span style="color:rgb(0,0,0);font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;margin:0px;padding:0px;border:0px;vertical-align:baseline;outline:0px">!</span></div><div><font color="#000000"><span style="background-color:rgb(255,255,255)"><span style="margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"> </span></span></font><div><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">MemBrain</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">-seg is the product of a great collaboration with Alister Burt </span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">(MRC LMB </span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">/ Genentech</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">) and Kevin Yamauchi </span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">(ETH Zürich</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">)</span><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px">.</span></div><div><span style="color:rgb(0,0,0);font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;margin:0px;padding:0px;border:0px;vertical-align:baseline;outline:0px"><br></span></div><div><br></div><div><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><span style="margin:0px;padding:0px;border:0px;vertical-align:baseline;outline:0px">Best wishes,</span></span></div><div><span style="color:rgb(0,0,0);margin:0px;padding:0px;border:0px;font-family:"gg sans","Noto Sans","Helvetica Neue",Helvetica,Arial,sans-serif;vertical-align:baseline;outline:0px"><span style="margin:0px;padding:0px;border:0px;vertical-align:baseline;outline:0px">Lorenz, Simon, Ben, Tingying, and the rest of the MemBrain team</span></span></div></div></div></div></div></div></div>