[ome-users] Question regarding your ImageJ Macro for Bio-Formats : "basicMetadata.txt"

[Curtis Rueden]

Hi Fatima,

Thanks for your inquiry. I am CCing the ome-users mailing list in my reply,
since that is the best place to get support for Bio-Formats.

> When I run the macro, it DOES NOT work for OIB images in the SAME
> directory. For example, look at the following information from the log
> window. It gives the same information for Image0001 and Image0002
> since they exist in a common directory. Note that the FOCAL PLANE
> COUNT is the same (which is incorrect).

The problem is very likely that Bio-Formats is trying to group your files
into a single dataset, since they have very similar names (which differ
only in numbering). There are multiple ways to avoid the issue:

1) The Bio-Formats macro extensions (functions starting with "Ext") are
intended to be a high-level convenience, and as such use the file stitching
logic by default, which is what performs the numerical grouping. You can
try disabling the file stitcher by adding the following line to the start
of the macro:

    Ext.setGroupFiles(false)

2) Alternately, it is enough to rename the files so their names do not
match a common template aside from numbers; e.g., "ImageA_AO_PI.oib" and
"ImageB_AO_PI.oib" would likely work.

If you continue to have trouble, please use "Reply to All" for additional
assistance.

Regards,
Curtis


On Thu, Mar 14, 2013 at 4:26 PM, Merchant, Fatima A <fmerchan at central.uh.edu
> wrote:

> Dear Curtis:
>
> Please may I request your assistance with the following macro that you
> wrote for Bio_Formats (attached)
>
> // basicMetadata.txt
> // Written by Curtis Rueden
> // Last updated on 2008 May 6
> // Uses Bio-Formats to print the chosen file's basic metadata to the Log.
>
> When I run the macro, it DOES NOT work for OIB images in the SAME
> directory.
> For example, look at the following information from the log window. It
> gives the same information for Image0001 and Image0002 since they exist in
> a common directory.
> Note that the FOCAL PLANE COUNT is the same (which is incorrect).
>
> /Users/merchant/Islet_Apoptosis/Images/Image0001_AO_PI.oib
> Series #0: image resolution is 512 x 512
> Focal plane count = 23
> Channel count = 3
> Time point count = 2
> /Users/merchant/Islet_Apoptosis/Images/Image0002_AO_PI.oib
> Series #0: image resolution is 512 x 512
> Focal plane count = 23
> Channel count = 3
> Time point count = 2
>
> However if I move one of the images to a DIFFERENT directory, the macro
> works accurately.
> Note that the FOCAL PLANE COUNT is the CORRECT, but I had to move one of
> the images to a different directory.
>
> /Users/merchant/Islet_Apoptosis/Images/Image0001_AO_PI.oib
> Series #0: image resolution is 512 x 512
> Focal plane count = 23
> Channel count = 3
> Time point count = 1
> /Users/merchant/Islet_Apoptosis/Image0002_AO_PI.oib
> Series #0: image resolution is 512 x 512
> Focal plane count = 19
> Channel count = 3
> Time point count = 1
>
> Please can you comment on if this can be fixed so that I can accurately
> read the information from multiple images in the same directory.
>
> Any and all help is very greatly appreciated.
>
> Thanks,
> Fatima
>
> <><><><><><><><><><><><><><><<><><><><><><><><><><><>
>
> Fatima Merchant, Ph.D.
> Assistant Professor
> Dept. of Engineering Technology
> Biotechnology Program
> College of Technology, T2 394
> University of Houston
> Mail: TECH II 4020
> 4800 Calhoun Road
> Houston, TX 77204
> Tel: 713-743-8292
> Fax: 713-743-4032
> Email: fmerchant at uh.edu
>
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