<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><blockquote type="cite"><div><br>Hi Ruben,<br></div></blockquote><div><br></div><div>Hi Melissa, I understand that mine was not an ScanR specific question, but I have to detail a bit more what I believe an issue.</div><div><br></div><blockquote type="cite"><div>The pixel type recorded by the ScanR software is stored in each of the<br>TIFF files. The above code retrieves the pixel type stored in the<br>first TIFF file; later on, that pixel type is assigned to each well<br>and field. So for the purposes of importing into OMERO, you should<br>not need to convert int16 images to uint16 - Bio-Formats will detect<br>whether or not the images are signed.</div></blockquote><div><br></div><div>With images from this microscope Pixel type = uint16 is auto detected, but they are all signed 16 bit, we know this with precision.</div><div><div><br></div><div>Then the files are not properly auto-detected, or the files are not consistent themselves, next is the output of ./showinf</div><div><br></div><div><div>Checking file format [Olympus ScanR]</div><div>...</div><div><div>Series count = 54</div><div>Series #0:</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Image count = 25</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>RGB = false (1)</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Interleaved = false</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Indexed = false (true color)</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Width = 1344</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Height = 1024</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>SizeZ = 1</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>SizeT = 25</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>SizeC = 1</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Thumbnail size = 128 x 97</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Endianness = intel (little)</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Dimension order = XYCTZ (uncertain)</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Pixel type = uint16</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Metadata complete = false</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>Thumbnail series = false</div></div></div><div><br></div></div><div><br></div><div>16 signed bit images display completely out of range, far too bright only in light grey (also with ./showinf).</div><div><br></div><div>Can we do something about it, to have "int16" stored would be correct.</div><br><blockquote type="cite"><div><br>The only assumption is that every well and field has the same pixel<br>type - if you know of a case where that assumption is incorrect,<br>please let me know<font class="Apple-style-span" color="#006312"><font class="Apple-style-span" color="#144FAE"><br></font></font></div></blockquote><div><br></div><div>All them are signed so far.</div><br><div><br></div><div>Thanks for your understanding, </div><div><br></div><div>Ruben</div><br><blockquote type="cite"><div><br>Regards,<br>-Melissa<br><font class="Apple-style-span" color="#000000"><font class="Apple-style-span" color="#144FAE"><br></font></font></div></blockquote><br><blockquote type="cite"><div>On Thu, Nov 26, 2009 at 11:27 AM, Rubén Muñoz <<a href="mailto:ruben.munoz@embl.de">ruben.munoz@embl.de</a>> wrote:<br><blockquote type="cite">Hello Melissa,<br></blockquote><blockquote type="cite">Your ScanR importer has loaded tons of datasets in our premises. We are<br></blockquote><blockquote type="cite">concerned that ScanR software is storing signed bit images, but part of the<br></blockquote><blockquote type="cite">code reads:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> reader = new MinimalTiffReader();<br></blockquote><blockquote type="cite"> reader.setId(tiffs[0]);<br></blockquote><blockquote type="cite"> int sizeX = reader.getSizeX();<br></blockquote><blockquote type="cite"> int sizeY = reader.getSizeY();<br></blockquote><blockquote type="cite"> int pixelType = reader.getPixelType();<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I cannot say how ScanR tells the sample bit representation, in this lab we<br></blockquote><blockquote type="cite">are used to convert the images from int16 to uint16 before processing them,<br></blockquote><blockquote type="cite">actually thats the way we keep on doing this.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Will be more convenient if the importer would store the proper value, but I<br></blockquote><blockquote type="cite">also would like to ask your opinion, since you are the expert.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">A different question would be if the 'real' number of bits used have a place<br></blockquote><blockquote type="cite">in OMERO metada, for example for many microscopes this is 12 bits.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Regards,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">Rubén Muñoz<br></blockquote><blockquote type="cite">European Molecular Biology Laboratory<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote></div></blockquote></div><br></body></html>