[ome-users] problems in opening a subset of images

[Melissa Linkert]

Hi Joaquim,

> I'm trying to use Bio-Formats Importer to open a subset of images. It should be really easy but I failed to succeed after checking all the documentation available.
> The four images I have attached to this e-mail are contained in a single folder.
> I want to open the subset of images containing "002002" in its name ("002002001.flex" and "002002001.flex").
> The easiest would be to drag and drop the first image in the folder into FIJI's.  This would open the Bio-Formats Import Options. If no option was ticked I would get the Bio-Formats Series Options in which I would choose the 2 images to open. However, this I cannot do because my original image folder contains 1500 images, resulting in a long waiting time.
> My best option seems to tick on "Group files with similar names" and try to instruct Bioformats to open only the images containing "002002" in its name. This is where I got stuck!!!
> I have tried every option every way but couldn't succeed.
> Can anyone help me this way or any other???

The "Open files individually" option should help - this will open only
the selected file, and so should be much faster.

Using the "Open files individually" option together with "Group files
with similar names" should solve this in theory, but unfortunately there
is a problem with using the two options together:

https://trac.openmicroscopy.org/ome/ticket/12941

You have been CC'd on that ticket (let us know if you prefer otherwise);
until it is fixed, the easiest thing to do would be to use a macro to
repeatedly call the Bio-Formats Importer on each of the desired files.

Regards,
-Melissa

On Mon, Jun 22, 2015 at 10:16:46AM +0000, Soriano.Joaquim wrote:
> Hi Everyone!
> I'm trying to use Bio-Formats Importer to open a subset of images. It should be really easy but I failed to succeed after checking all the documentation available.
> The four images I have attached to this e-mail are contained in a single folder.
> I want to open the subset of images containing "002002" in its name ("002002001.flex" and "002002001.flex").
> The easiest would be to drag and drop the first image in the folder into FIJI's.  This would open the Bio-Formats Import Options. If no option was ticked I would get the Bio-Formats Series Options in which I would choose the 2 images to open. However, this I cannot do because my original image folder contains 1500 images, resulting in a long waiting time.
> My best option seems to tick on "Group files with similar names" and try to instruct Bioformats to open only the images containing "002002" in its name. This is where I got stuck!!!
> I have tried every option every way but couldn't succeed.
> Can anyone help me this way or any other???
> Thank you very much in advance!!!
> 
> Joaquim Soriano Felipe.
> Confocal Microscopy Unit
> Spanish National Cancer Research Centre (CNIO)
> Melchor Fernández Almagro,3, E-28029 Madrid, Spain
> Phone  + 34 917 328 000, exts.: 3161, 3162. jsoriano at cnio.es<mailto:jsoriano at cnio.es>
> 





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