<div dir="ltr">In fact I have checked axes order with tifffile.py so it may not be the same order as BF. However it does not matter here because I know these file does not contain Z axes (only T) from metamorph. So I think BF detect T=5 and Z=2 while it should detect T=10 and Z=1.</div>
<div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br>Hadrien Mary<div><br></div><div>Ph.D student in Biology</div><div>Tournier-Gachet Team</div><div>CNRS - LBCMCP - UMR 5088<div><div><br></div><div><div>
Université de Toulouse - Bât. 4R3B1</div><div>118, route de Narbonne - 31062 Toulouse</div></div></div></div></div></div>
<br><br><div class="gmail_quote">On Wed, Jul 30, 2014 at 12:13 PM, Roger Leigh <span dir="ltr"><<a href="mailto:rleigh@dundee.ac.uk" target="_blank">rleigh@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="">On 29/07/14 14:03, Hadrien Mary wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I may have a bug with some .stk file. I paste here the bug from<br>
Fiji Bugzilla:<br>
<br>
****<br>
Note that I use a recent IJ/Fiji version (and the bug has also been<br>
noticed with an older IJ version few months ago).<br>
<br>
Some .stk files are not correctly detected by BF and IJ open them with<br>
two axes (Z and T) while only one exist. Examples (axes order is T, Z,<br>
X, Y, C) :<br>
<br>
- file1.stk : real shape = (10, 1, 264, 268, 1), BF detected shape = (5,<br>
2, 264, 268, 1)<br>
</blockquote>
<br></div>
Current dev_5_0:<br>
<br>
Width = 268<br>
Height = 264<br>
SizeZ = 2<br>
SizeT = 5<br>
SizeC = 1<div class=""><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
- file2.stk (with several channels): real shape = (10, 1, 139, 224, 3),<br>
BF detected shape = (5, 2, 139, 224, 3)<br>
</blockquote>
<br></div>
Width = 224<br>
Height = 139<br>
SizeZ = 2<br>
SizeT = 5<br>
SizeC = 3 (effectively 1)<div class=""><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Both files have been saved from Metamorph after a z-projection (I bet<br>
the issue comes from here).<br>
<br>
They open well on different Metamorph versions and also tifffile.py lib<br>
detects the correct shapes.<br>
<br>
Both stk are in the attachment file called stk_files.zip<br>
***<br>
<br>
Original bug can be found here :<br>
<a href="http://fiji.sc/bugzilla/show_bug.cgi?id=868" target="_blank">http://fiji.sc/bugzilla/show_<u></u>bug.cgi?id=868</a> (it has been closed since it<br>
seems to be a bug only related to BF).<br>
<br>
You can find attachment file on the Fiji Bugzilla.<br>
</blockquote>
<br></div>
Thanks. Just to double check your figures above, are the X and Y<br>
transposed; the TIFF data and Bio-Formats show them to be the other way<br>
around. Are all the other dimensions correct in the axes order above?<br>
<br>
<br>
<br>
Thanks,<br>
Roger<br>
--<br>
Dr Roger Leigh -- Open Microscopy Environment<br>
Wellcome Trust Centre for Gene Regulation and Expression,<br>
College of Life Sciences, University of Dundee, Dow Street,<br>
Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
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</blockquote></div><br></div>