<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> Hello,</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I try to convert the LSM files (Zeiss) to VTK file format.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I had a look on the different Library of VTK/ITK</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and i saw that on ITK->Code->IO, there is a file call itkLSMImageIO (.h and .cxx) which read a LSM file.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">But i have a problem when i read the LSM file and save it in a VTK format, it saves only the first image of the stack. </DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">It create all the different images in z and make a VTK matrix with all this stack, but only the first image on this stack is written, the other are all black ...</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; ">Have you got an Idea, i think it's a problem of the reader.<BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2">I use the file <FONT class="Apple-style-span" color="#000000" face="Lucida Grande" size="3"><SPAN class="Apple-style-span" style="font-size: 12px;">itkLSMImageIOTest.cxx </SPAN></FONT></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> typedef</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> itk::RGBPixel< </SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">unsigned</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">char</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> > </SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">InputPixelType;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">typedef</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> itk::Image< InputPixelType, </SPAN></FONT><FONT class="Apple-style-span" color="#0000FF" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">3</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> > InputImageType;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">typedef</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> itk::ImageFileReader< InputImageType > ReaderType;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">typedef</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> itk::LSMImageIO ImageIOType;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> ReaderType::Pointer reader = ReaderType::New();</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">reader->SetFileName( filename );</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">ImageIOType::Pointer lsmImageIO = ImageIOType::New();</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">reader->SetImageIO( lsmImageIO );</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">reader->Update();</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> <FONT class="Apple-style-span" color="#760F50"></FONT></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"><FONT class="Apple-style-span" color="#760F50"> typedef</FONT> itk::ImageFileWriter< InputImageType > WriterType;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">WriterType::Pointer writer = WriterType::New();</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">writer->SetFileName( outfilename );</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">writer->SetInput( reader->GetOutput() );</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> writer->Update();</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> </SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">lsmImageIO->Print(std::cout);</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV></BODY></HTML>