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<p class="MsoNormal"><span lang="EN-US">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">we have ND2 files that contain several stage (XY) positions. At every stage position, a few stacks of a few tens of planes over a few channels and a few time points are acquired.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Bio-Formats (5.0.0) seems to get all dimensions correctly, but then it misinterprets the sequences of planes and redistributes them over the wrong axes.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Specifically, even though the number of series in the file match the number of stage positions, the T, C, and Z dimensions match the ones in each series, when you look at the opened stacks you see that it contains segments
from different stage positions. Swapping dimensions while opening does not help, because you can do it for planes within a series; here the problem is that the planes are read “horizontally” over stage positions.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I have a good example file if you would like to have it (a.k.a. where can I upload it ;-) ?)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks a lot in advance<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">a2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">----<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">Dr. Aaron Ponti<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">Software and Data Management Engineer<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">Single Cell Unit<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:DE-CH">Department of Biosystems Science and Engineering (D-BSSE)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">ETH Zürich<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">Office 2.24<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">Mattenstrasse 26<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">4058 Basel, Switzerland<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">aaron.ponti@bsse.ethz.ch<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:DE-CH">+41 61 387 33 74<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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