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<p class="MsoNormal">Hi All,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have been trying to register Z-stacks of Zebrafish using the SPIM plugin with various concentrations of beads but despite everything I try I cannot get the beads to match with different angles.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am not sure if this is because of the light sheet not being aligned properly (I am calculating the PSF very soon and will re-align the system from scratch) or due to sample prep etc. I have corrected bead drifting (as this was evident
in low concentrations of agarose) and I am pretty sure the xy and z resolution numbers are correct. I will attempt the Multiview reconstruction package, FluoRender or even ClearVolume but without bead registration working I am not sure if that will work either.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Would it be possible that if the FEP tube is not straight, the manual positioning of the next angles would misalign bead registration? I have also thought that as the embryo fills up the tube, I am not getting enough volume of beads on
either side of the stack for bead registration?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If anyone has had difficulty in this or have done work on Zebrafish with SPIM I would really appreciate any help.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Kind regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dylan<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB">Dylan Windell<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB">Postgraduate Researcher<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB"><a href="http://business-school.exeter.ac.uk/research/areas/centres/isr/"><span style="color:#1F497D;text-decoration:none">College</span></a> of Life and Environmental
Sciences<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB">University of Exeter, Geoffrey Pope<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB">Stocker Road, Exeter EX4 4QD, UK
<o:p></o:p></span></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB">phone: +44 (0) 7596725056<o:p></o:p></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB">email:
<u><a href="mailto:dw388@exeter.ac.uk"><span style="color:blue">dw388@exeter.ac.uk</span></a></u><o:p></o:p></span></i></p>
<p class="MsoNormal"><o:p> </o:p></p>
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