Hi Frans,<br><br>Sorry for the delay in my reply, but I was waiting to discuss your question with the other OME developers on our weekly conference call.<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">Is</font></span><span lang="en-au"></span><span lang="en-us"></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">it possible to convert 1-bit PNG files (cell-boundaries as a binay image) to 1-bit OME.Tiff files?</font></span><span lang="en-au"></span><span lang="en-us"></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">If I use the bfconvert command line tool, it ends up as a</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">UINT8 image</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">…</font></span><span lang="en-au"></span><span lang="en-us"></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">The (compressed) PNG file is only 4 K, the Tiff becomes 3900 K</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">.</font></span><span lang="en-au"></span><span lang="en-us"></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial"></font></span></p></div></blockquote><div><br>Yes, as you point out, right now the conversion expands the data to uint8. We definitely want to support other bit depths, including 1-bit, 2-bit and 4-bit packed. Doing so involves adding new pixel types to the OME data model, and making some changes to the Bio-Formats API. My current idea is to have a flag in IFormatReader that instructs Bio-Formats whether to expand to the nearest byte boundary -- i.e., when set, binary data would become uint8, and when left unset, data would remain packed. This way, applications like OMERO.importer can continue to function without needing to immediately add support for binary data to the OMERO server, and we can also go ahead and improve the ImageJ importer plugin to read in binary data without expansion into ImageJ. This change, together with some improvements to the TIFF writer, would also allow you to convert 1-bit data to OME-TIFF format. Eventually OMERO.server could support the other types if we decide that's the route we want to go.<br>
<br>Regardless, we want to provide a solution that does not take orders of magnitude more space than necessary. We are still finalizing our plan and will file appropriate Trac tickets soon.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">I have individual overlay files for the CellBodies, the Nuclei and the Neurites.</font></span><span lang="en-au"></span><span lang="en-us"></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">Ultimately, I want to import the</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">se PNG</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial"> file</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">s</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial"> as</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">new</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">"</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">Channel</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">s</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">"</font></span><span lang="en-au"></span><span lang="en-us"></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">of an existing file (with already 2 channels)</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">to show it as an</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">"</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">overlay</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">"</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial"> in the Insight Viewer.</font></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">Are there easier ways to do this ?</font></span></p>
</div></blockquote></div><br>I also agree with Ghislain Bonamy that ultimately, it would be good to somehow support binary images as masks within the ROI model, but that is still a ways off.<br><br>-Curtis<br><br><div class="gmail_quote">
On Mon, Jan 5, 2009 at 8:50 AM, Cornelissen, Frans [PRDBE] <span dir="ltr"><<a href="mailto:FCORNELI@its.jnj.com" target="_blank">FCORNELI@its.jnj.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
<ul><ul><ul><ul>
<p align="left"><span lang="en-au"><font color="#000080" size="2" face="Arial">All,</font></span><span lang="en-au"><font color="#000080" size="2" face="Arial"> </font></span></p>
<p align="left"><span lang="en-au"><font color="#000080" size="2" face="Arial">best wishes for 2009</font></span><span lang="en-au"></span></p>
</ul></ul></ul></ul>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">Is</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial"></font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">it possible to convert 1-bit PNG files (cell-boundaries as a binay image) to 1-bit OME.Tiff files?</font></span><span lang="en-au"></span><span lang="en-us"></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">If I use the bfconvert command line tool, it ends up as a</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">UINT8 image</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">…</font></span><span lang="en-au"></span><span lang="en-us"></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">The (compressed) PNG file is only 4 K, the Tiff becomes 3900 K</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">.</font></span><span lang="en-au"></span><span lang="en-us"></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">I have individual overlay files for the CellBodies, the Nuclei and the Neurites.</font></span><span lang="en-au"></span><span lang="en-us"></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">Ultimately, I want to import the</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">se PNG</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial"> file</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">s</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial"> as</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">new</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">"</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">Channel</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">s</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">"</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial"></font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">of an existing file (with already 2 channels)</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">to show it as an</font></span><span lang="en-au"></span><span lang="en-us"> <font color="#000080" size="2" face="Arial">"</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">overlay</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial">"</font></span><span lang="en-au"></span><span lang="en-us"><font color="#000080" size="2" face="Arial"> in the Insight Viewer.</font></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">Are there easier ways to do this ?</font></span></p>
<br>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">Thanks,</font></span></p>
<p align="left"><span lang="en-us"><font color="#000080" size="2" face="Arial">Best regads, frans</font></span><span lang="en-au"></span><span lang="en-us"></span></p>
</div>
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