On Wed, May 13, 2009 at 2:52 PM, Matthew Brett <span dir="ltr"><<a href="mailto:matthew.brett@gmail.com">matthew.brett@gmail.com</a>></span> wrote:<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;">
> or 3. Can it also read other image formats:<br><div class="im">
><br>
> (data4,meta4) = somepackage.load('help.tif') # common img formats<br>
<br>
</div>No... I suppose it could, via PIL or something, but that would only<br>
make sense if the TIFF was a volume.<br>
</blockquote><div><br>Thanks Matthew. If this were to make it's way to scipy, I think it
would be good for it to read stacked tiff's. That's the format that's
used by molecular biologists and neuroscientists to store confocal
microscopy and other imaging data.<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;"><br>
The idea is - post sprint - that the image object should insist on at<br>
least 3 dimensions...<br>
</blockquote><div><br>A 2D image is a volume with the 3rd dimension set to 1. So if I extracted slices from a volume would I have to do:<br><br>someotherpackage.save(my2Dslice,'canIbea3dvol.dcm')<br><br>instead of <br>
<br>medvol.save(my2Dslice,'iama3dvol.dcm') <br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
So, yes, I think it's medical volume.</blockquote><div><br>I think my general point is that if this was purely a neuroimaging thing, it should remain within NiPy. However, if it is more generally applicable to medical images, then it should seriously consider a framework in which it can support other common volume-like formats.<br>
<br></div></div>Cheers,<br><br>Satra<br>