<div dir="ltr">Hi Philipp,<div><br></div><div>it seems that TFS has recently removed the XML string with defects from the 65100 tiff tag inside EER files. Besides looking for zero pixels in the gain file another option is to check C:/Titan/Data/EF-Falcon4/SensorDefects.xml file. 0,0 should be in the bottom left corner.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt">Best regards,<br>Grigory</span></font></div><div style="color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt"><br></span></font></div><div style="color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt">--------------------------------------------------------------------------------</span></font></div><div style="color:rgb(0,0,0)"><span style="font-size:12.8px">Grigory Sharov, Ph.D.</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">MRC Laboratory of Molecular Biology,</span><br style="font-size:12.8px"><span style="font-size:12.8px">Francis Crick Avenue,</span><br style="font-size:12.8px"><span style="font-size:12.8px">Cambridge Biomedical Campus,</span><br style="font-size:12.8px"><span style="font-size:12.8px">Cambridge CB2 0QH, UK.</span><br style="font-size:12.8px"><span style="font-size:12.8px">tel. </span><a href="tel:+44%201223%20267228" value="+441223267542" style="color:rgb(17,85,204);font-size:12.8px" target="_blank">+44 (0) 1223 267228</a></div><div style="color:rgb(0,0,0)"><span style="font-size:12.8px">e-mail: </span><a href="mailto:gsharov@mrc-lmb.cam.ac.uk" style="color:rgb(17,85,204);font-size:12.8px" target="_blank">gsharov@mrc-lmb.cam.ac.uk</a><br></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jan 11, 2024 at 10:57 AM Philipp Sebastian Erdmann <<a href="mailto:philipp.erdmann@fht.org">philipp.erdmann@fht.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<b>Dear All,</b>
<div><br>
</div>
<div>I recently tried reading the defects from the .gain file of our Falcon4i.</div>
<div><br>
</div>
<div>However, the xml embedded in the .gain reads as:</div>
<div><br>
</div>
<div><span dir="ltr"><defects><!-- Defects file not present --></defects></span></div>
<div><span dir="ltr"><br>
</span></div>
<div><span dir="ltr">Is the is bug in the software? Maybe it is not yet implemented by TFS?</span></div>
<div><span dir="ltr"><br>
</span></div>
<div>Are there other ways to extract it?</div>
<div><br>
</div>
<div>I know the .gain zeros are the defects, but is this not an issue if you take the reciprocal?</div>
<div><br>
</div>
<div>1/0 = 🤯</div>
<div><br>
</div>
<div>We’re trying to figure out which software does best in processing .eer files of tomograms.</div>
<div><br>
</div>
<div>(Low dose; ca 3 e/Å2)</div>
<div><br>
</div>
<div>Relion looks perfect but does not produce 1/2 stacks for denoising.</div>
<div><br>
</div>
<div>Warp and MC3 produce 1/2 stacks, but I can see artifacts in the pixel substitution.</div>
<div><br>
</div>
<div><br>
</div>
<div>Thanks for your help!</div>
<div><br>
</div>
<div><br>
</div>
<div>Philipp.</div>
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