[ome-users] Issue with opening CZI files for a multi-well experiment

[Balaji Ramalingam]

Hi,

Thank you for reporting your issue,
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'.

There are potentially 2 work-arounds for this problem.

1) Please check the following,
'Edit > Options > ImageJ2'

[cid:6B940D22-7B62-46C2-8F82-BF46F55404CF]
And check if the SCIFIO option is un/checked.

If its checked, you don't get the 'import window' with options suggested below

>>" 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."

If the same is unchecked you do get the import window with the options.

2) The second option is a more straight forward one,
Please use 'Plugins>Bio-Formats Importer'

And this should throw up the 'import window' with the options as mentioned previously.

Either option should work. Please do let us know if this doesn't solve your issue.

Best,
Balaji



__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Alice Schoenauer Sebag <alice.schoenauer at polytechnique.org<mailto:alice.schoenauer at polytechnique.org>>
Date: Tuesday, 1 July 2014 14:36
To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: [ome-users] Issue with opening CZI files for a multi-well experiment

Hello,

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).

More precisely, in the folder are the files:
- Fluo_1.czi: header file
- Fluo_1(1).czi for well 1
- Fluo_1(2).czi for well 2
- etc.

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.

Now, I can still run the command IJ.open(file), or use the Gui to open the header file or individual well file, but :
- in the first case, whichever well file I open, IJ.open(file) opens the first well file
- in the second case, no window pops up and only the first well file opens, whatever I do.

Messages in the shell:
SLF4J: Class path contains multiple SLF4J bindings.
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]
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]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]

I just want to open each CZI file to measure the mean intensity and record it.

Thanks a lot for your help,
Regards,
Alice Schoenauer Sebag

The University of Dundee is a registered Scottish Charity, No: SC015096
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