<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Correction: LabTek is 12 columns and 32 rows, not the opposite.
</div>
<div><br></div><div>Sorry</div><br><div><div>On Dec 16, 2009, at 10:53 AM, Rubén Muńoz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><blockquote type="cite"><div>Hi Ruben,<br><br></div></blockquote><div><br></div><div>Hi Melissa</div><blockquote type="cite"><div><br>This is expected; your original ScanR data has 16 bits per pixel, but<br>Bio-Formats can only write JPEGs with 8 bits per pixel.<br></div></blockquote><div><br></div><div>That's very fine because we do not want to loose quality during the conversion.</div><blockquote type="cite"><div><font class="Apple-style-span"><br></font>Exporting signed data to PNG should work if you update to the latest<br>trunk build. The pixel data is converted from signed to unsigned<br>(since PNG does not support signed pixel types), so the pixel type of<br>the converted PNG will be 'uint16'.<br></div></blockquote><div><br></div><div>Tried this, the results was very satisfactory. :)</div><div><br></div><div>I have one more concern about bioformats, which is again ScanR specific.</div><div><br></div><div>It is great that the importer currently supports different not labelled layouts:</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "><span style="color: #900868">if</span> (wellRows * wellColumns == 0) {</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> <span style="color: #900868">if</span> (wellLabels.size() <= 96) {</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> wellColumns = 12;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> }</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> <span style="color: #900868">else</span> <span style="color: #900868">if</span> (wellLabels.size() <= 384) {</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> wellColumns = 24;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> }</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> wellRows = wellLabels.size() / wellColumns;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; "> <span style="color: #900868">if</span> (wellRows * wellColumns < wellLabels.size()) wellRows++;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; ">}</div></div><div><br></div><div>There's in fact a third layout (LabTek) which is 12 rows and 32 columns. At the moment this layout is importing because the wells are labeled: A1 to L32</div><div><br></div><div>You may notice that the naming convention is the opposite for this layout. Below is the current ScanR naming convention:</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; ">store.setPlateRowNamingConvention(<span style="color: #471cfe">"A"</span>, 0);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 11px/normal Monaco; ">store.setPlateColumnNamingConvention(<span style="color: #471cfe">"1"</span>, 0);</div></div><div><br></div><div> - Would it possible to detect the LabTek layout and apply a different naming convention? A I said, it has different number of columns and rows than the normal 384 Plates.</div><div> - In addition would it be possible to give the Spot number (1 - 384) to the well name for that particular layout? (something like <span class="Apple-style-span" style="font-family: Monaco; font-size: 11px; ">store.setImageName(new String(i), i);)</span></div><div><br></div><div>I think that these are minor changes but I could upload corresponding datasets (from LabTeks) under request. By now I attach an experiment_descriptor.xml for one of this 384 LabTeks.</div><div><br></div><div><br></div><div></div></div></div><span><experiment_descriptor.xml></span><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div></div><div><br></div><div>Sincerely grateful.</div><div><br></div><div>Merry christmas!</div><div><br></div><div>Rubén</div><br><blockquote type="cite"><div><br>Regards,<br>-Melissa<br></div></blockquote></div><br></div></blockquote></div><br></body></html>