Posted by
ctrueden on
Aug 10, 2007; 3:06pm
URL: http://imagej.273.s1.nabble.com/macro-using-LOCI-Bio-Formats-Importer-tp3698641p3698642.html
Hi Christophe,
I'm glad Bio-Formats is useful to you. If I understand correctly, the
problem is that there is currently no way to script, within a macro,
that you want *all* image series? Such an option would be
straightforward for us to add.
More complex would be to include series based on certain criteria,
such as single image, or specific resolutions. In that case, the
Bio-Formats library has all the power you need, but it is not all
accessible directly from the ImageJ plugin -- it would probably be
easier to write your own plugin. Unfortunately, a lot of useful
ImageJ-related logic within Bio-Formats is embedded directly in the
Importer plugin, rather than modularized for reuse by other plugins.
But we can fix that.
If you have the time, I would like to hear more about your
requirements off-list, so that we can help improve Bio-Formats to meet
your needs.
-Curtis
On 8/9/07, lechristophe <
[hidden email]> wrote:
> Dear ImageJ specialists,
>
> Ijust installed the latest LOCI Bio Formats tool and it's great ! I use it
> to import .LIF Leica experiments. I would like to do the following with a
> macro (without user interaction !) :
>
> 1- Open sequentially all XYZ stacks (separated channels) in the LIF file
> using the Bio Formats Importer
> 2- For each stack, Z-project the stack (Maximum Projection) and possibly
> other manipulation (filtering, colorizing, etc...)
> 3- For each stack, save the resulting projection (with all spatial and
> naming infos) in the experiment folder
>
> The problem is that I don't see how I can do the first step within a macro.
> If I record the Bio Format Importer using the macro recorder, I see that I
> can call the importer, but I have to specify the names of the different
> series inside the .LIF.
> Is there some java function in the plugin that could return infos about
> what's contained in the .LIF file (name of stacks, number of channels,
> etc...) ? I could the store the infos and use them for iterative use of the
> importer.
>
> What do you think ? Would it be better with a plugin than with a macro ?
>
> Christophe
> --
> View this message in context:
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>