[ome-users] [Software Feedback] opening Olympus APL file

[Curtis Rueden]

Hi Clare,

> And LOCI sill cannot read the metadata in the apl file so i have no
> idea which experiment is in each tif file!

Can you please use the Help > Upload Sample Image command of Fiji to upload
the problematic data? You can ctrl+click the folder containing the dataset
and choose "Compress" to create a ZIP file which can be uploaded. Then we
can investigate the issue further.

Thanks,
Curtis


On Tue, Dec 4, 2012 at 1:10 PM, Bergson, Clare
<CBERGSON at georgiahealth.edu>wrote:

>  dear Curtis, thanks so much for your reply. the issue might be that i'm
> using a mac computer. a colleague told me to look for the hidden tif files
> associated with the olympus apl database. i was able to see these hidden
> files on finder with a program i downloaded. however, LOCI doesn't see them
> even though the hidden files revealer program is open.  Any suggestions?
> And LOCI sill cannot read the metadata in the apl file so i have no idea
> which experiment is in each tif file! Any suggestions? thanks so much for
> looking into this.  all the best, clare
>
>  On Nov 27, 2012, at 3:48 PM, Curtis Rueden wrote:
>
> Hi Clare,
>
>   > What boxes do i check to open the database?
>
>  Bio-Formats will parse metadata from the database and store it in a
> simple table of key/value pairs known as the "original metadata" table. To
> see this table, check the "Display metadata" option, or run "Image > Show
> Info" from the menu after loading your image(s).
>
>  Bio-Formats also standardizes applicable metadata to the OME standard.
> Not all information will be standardized; only those things that have a
> place in the standard will be converted. To see the information in this
> standardized form, check the "Display OME-XML metadata" option.
>
>  For more about Bio-Formats metadata handling, see:
>     https://www.openmicroscopy.org/site/support/bio-formats/about.html
>
>  > Finally, is there a way to go from opening the database to opening a
> > particular image series (experiment)?
>
>  After clicking OK to the first dialog, Bio-Formats will present you with
> another dialog titled "Bio-Formats Series Options" in the event of multiple
> image series being detected (if there is only one series, it will simply
> open it). Using this second dialog box, you can select whichever series you
> wish to be opened.
>
>  Alternately, if you want them all to be opened, you can check the "Open
> all series" option on the first "Bio-Formats Import Options" dialog to
> bypass the second dialog box.
>
>  If Bio-Formats is missing metadata, or not reading your image pixels
> and/or series correctly, please let us know and we will be happy to
> investigate the issue.
>
>  Regards,
> Curtis
>
>
> On Mon, Nov 26, 2012 at 4:26 PM, Clare Bergson <cbergson at georgiahealth.edu
> > wrote:
>
>> LOCI is running as a plugin on Image J on my computer.  I'm trying to
>> open .apl Olympus database and associated image files. One question is is
>> on the 'BioFormats Import Options' screen.  What boxes do i check to open
>> the database? Finally, is there a way to go from opening the database to
>> opening a particular image series (experiment)? If so, how? If you have you
>> successfully loaded an .apl file into Image J with LOCI, I would be most
>> grateful for step by step instructions. thanks so much for your help. Clare
>>
>
>
>
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