<div dir="ltr">Hi Lee,<div><br></div><div><div>> For the IM3 reader, my naive idea was to package all 63 channels as</div><div>> one interleaved image, but I have a feeling that's 60 more than most</div><div>> software expects, but it would be very sad to run through the 200Mb</div>
<div>> file 63 times in order to get 63 planar images.</div></div><div><br></div><div>The way Bio-Formats handles this for the SDT file format, which has interleaved data of 16 channels or more, is indeed to report the channels as interleaved.</div>
<div><br></div><div>
Return a dimension order of XYCZT, and return true for isInterleaved().</div><div><br></div><div><a href="https://github.com/openmicroscopy/bioformats/blob/v5.0.3/components/formats-api/src/loci/formats/IFormatReader.java#L227-L239" target="_blank">https://github.com/openmicroscopy/bioformats/blob/v5.0.3/components/formats-api/src/loci/formats/IFormatReader.java#L227-L239</a><br>
</div><div><br></div><div>Bio-Formats has built-in tools to separate out the channels by buffering the relevant interleaved plane in memory. It's called ChannelSeparator:</div><div><br></div><div><a href="https://github.com/openmicroscopy/bioformats/blob/v5.0.3/components/formats-bsd/src/loci/formats/ChannelSeparator.java" target="_blank">https://github.com/openmicroscopy/bioformats/blob/v5.0.3/components/formats-bsd/src/loci/formats/ChannelSeparator.java</a><br>
</div><div><br></div><div>Regards,</div><div>Curtis</div><div><br></div><div>P.S. The SCIFIO API generalizes this much more, moving away from the hardcoded 5D OME data model in favor of the ImgLib2 N-dimensional data model. But unfortunately that API is still in flux.</div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Aug 26, 2014 at 11:48 AM, Lee Kamentsky <span dir="ltr"><<a href="mailto:leek@broadinstitute.org" target="_blank">leek@broadinstitute.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi all,<div>I've been working on the .IM3 format for the Perkin-Elmer Nuance multi-spectral microscope. It has 63 channels per pixel for the spectral data and the data is interleaved (and I thought it would be the most efficient to keep it that way). For the IM3 reader, my naive idea was to package all 63 channels as one interleaved image, but I have a feeling that's 60 more than most software expects, but it would be very sad to run through the 200Mb file 63 times in order to get 63 planar images.</div>
<div><br></div><div>Otherwise, it looks like an awesome machine. I am guessing that LOCI has been working with other multispectral imaging systems and might point me to a representative reader that I might use as a guide.</div>
<span><font color="#888888">
<div><br></div><div>--Lee</div></font></span></div>
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