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

[Alice Schoenauer Sebag]

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
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