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Re: [scipion-users] Removing empty particles
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From: Dmitry A. S. <sem...@gm...> - 2021-04-14 20:55:54
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<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72" style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal>Dear Carlos Oscar & Grigory,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Indeed, by empty particles I mean the projections that contain no information about studying sample – so the noised ones, not the ones with the ice (the default value in abovemention xmipp protocol it is 1.1).</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The problem I am tackling is the presence of many empty picked positions that somehow doesn’t classified out after 2D/3D.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>So I understood that I can measure the threshold with relion script that you pointed out.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>And I will try to pick better <span style='font-family:"Segoe UI Emoji",sans-serif'>😊</span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you both</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Kind regards,</p><p class=MsoNormal>Dmitry</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:sha...@gm...">Grigory Sharov</a><br><b>Sent: </b>Wednesday, April 14, 2021 3:39 PM<br><b>To: </b><a href="mailto:sci...@li...">Mailing list for Scipion users</a><br><b>Subject: </b>Re: [scipion-users] Removing empty particles</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi Dmitry,</p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I haven't used that protocol so can't comment on it. By empty particles do you mean completely black particles with 0.0 or some particles with noise inside? You could use relion_image_handler with the "--stats" option to find the former ones. </p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Getting rid of second ones is more difficult.</p></div><div><p class=MsoNormal><br clear=all></p><div><div><div><div><div><div><div><div><div><div><div><div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>Best regards,<br>Grigory</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:black'>--------------------------------------------------------------------------------</span><span style='color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>Grigory Sharov, Ph.D.<br><br>MRC Laboratory of Molecular Biology,<br>Francis Crick Avenue,<br>Cambridge Biomedical Campus,<br>Cambridge CB2 0QH, UK.<br>tel. </span><span style='color:black'><a href="tel:+44%201223%20267228" target="_blank"><span style='font-size:9.5pt;color:#1155CC'>+44 (0) 1223 267228</span></a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;color:black'>e-mail: </span><span style='color:black'><a href="mailto:gs...@mr..." target="_blank"><span style='font-size:9.5pt;color:#1155CC'>gs...@mr...</span></a><o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok <<a href="mailto:Sem...@gm..." target="_blank">Sem...@gm...</a>> wrote:</p></div></div><p class=MsoNormal style='margin-left:4.8pt'>Dear colleagues,<br><br><br>One more question about effective deletion of the empty particles in the dataset.<br><br>Correct me if I am wrong, but the dedicated tools for that purpose are: xmipp - eliminate empty classes // particles.<br><br>I would like to ask if there is a possibility to boost the processing speed of them? I am afraid that it is using only 1 MPI and in case of few millions particles the processing on 1 MPI can take few days.<br><br><br>Thank you<br><br>Sincerely,<br>Dmitry<br><br><br><br>_______________________________________________<br>scipion-users mailing list<br><a href="mailto:sci...@li..." target="_blank">sci...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/scipion-users" target="_blank">https://lists.sourceforge.net/lists/listinfo/scipion-users</a></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
