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<div>Hi,</div>
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<div>Thank you for reporting your issue,</div>
<div>I was able to reproduce the same locally. The main issue seems to be the inability to select ‘import options’ when you use ‘Fiji > Open’.</div>
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<div>There are potentially 2 work-arounds for this problem.</div>
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<div>1) Please check the following,</div>
<div>'Edit > Options > ImageJ2'</div>
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<div><img src="cid:6B940D22-7B62-46C2-8F82-BF46F55404CF" type="image/png"></div>
<div>And check if the SCIFIO option is un/checked.</div>
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<div>If its checked, you don’t get the ‘import window’ with options suggested below</div>
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<div>>>" I could also open the header file, and a window would pop up, asking me if I want the metadata, if a virtual stack should be used, etc. After clicking on ok, the header file would be analyzed, and a new window would pop up, asking me to select the
well (the "Series" as it was called in the window) or the wells that I was interested in.”</div>
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<div>If the same is unchecked you do get the import window with the options.</div>
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<div>2) The second option is a more straight forward one,</div>
<div>Please use 'Plugins>Bio-Formats Importer’</div>
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<div>And this should throw up the ‘import window’ with the options as mentioned previously.</div>
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<div>Either option should work. Please do let us know if this doesn’t solve your issue.</div>
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<div>Best,</div>
<div>Balaji</div>
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<div style="color: rgb(40, 40, 40);"><span style="background-color: rgb(255, 255, 255);">__________________</span></div>
<div style="color: rgb(40, 40, 40);">
<p style="margin-top: 0px; margin-bottom: 0px;">Mr Balaji Ramalingam</p>
<p style="margin-top: 0px; margin-bottom: 0px;">Software Developer<br>
</p>
<p style="margin-top: 0px; margin-bottom: 0px;">OME Team</p>
<p style="margin-top: 0px; margin-bottom: 0px;">College of Life Sciences</p>
<p style="margin-top: 0px; margin-bottom: 0px;">University of Dundee</p>
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<span style="font-weight:bold">From: </span>Alice Schoenauer Sebag <<a href="mailto:alice.schoenauer@polytechnique.org">alice.schoenauer@polytechnique.org</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 1 July 2014 14:36<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>[ome-users] Issue with opening CZI files for a multi-well experiment<br>
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<div dir="ltr">Hello,<br>
<br>
I do not manage to open CZI files that are related to well images of one experiment on a 48-well plate. FiJi is up to date, version 2.0.0-rc-6/1.49b, as well as Bioformats (5.0.2-DEV). Java version: 1.6.0_24(64bit).<br>
<br>
More precisely, in the folder are the files:<br>
- Fluo_1.czi: header file<br>
- Fluo_1(1).czi for well 1<br>
- Fluo_1(2).czi for well 2<br>
- etc.<br>
<br>
Before updating at the beginning of June 2014, I could open directly the files dealing with each well using the command in Jython : IJ.open(file). I could also do it using the Gui, and open each well file directly selecting it in the menu File > Open... . I
could also open the header file, and a window would pop up, asking me if I want the metadata, if a virtual stack should be used, etc. After clicking on ok, the header file would be analyzed, and a new window would pop up, asking me to select the well (the
"Series" as it was called in the window) or the wells that I was interested in.<br>
<br>
Now, I can still run the command IJ.open(file), or use the Gui to open the header file or individual well file, but :<br>
- in the first case, whichever well file I open, IJ.open(file) opens the first well file<br>
- in the second case, no window pops up and only the first well file opens, whatever I do.<br>
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Messages in the shell:<br>
SLF4J: Class path contains multiple SLF4J bindings.<br>
SLF4J: Found binding in [jar:file:/media/New/software2/downloads/unpacked/Fiji.app/jars/slf4j-log4j12-1.7.2.jar!/org/slf4j/impl/StaticLoggerBinder.class]<br>
SLF4J: Found binding in [jar:file:/media/New/software2/downloads/unpacked/Fiji.app/jars/logback-classic-1.0.9.jar!/org/slf4j/impl/StaticLoggerBinder.class]<br>
SLF4J: See <a href="http://www.slf4j.org/codes.html#multiple_bindings">http://www.slf4j.org/codes.html#multiple_bindings</a> for an explanation.<br>
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]<br>
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I just want to open each CZI file to measure the mean intensity and record it.<br>
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Thanks a lot for your help,<br>
Regards,<br>
Alice Schoenauer Sebag</div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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