macro using LOCI Bio Formats Importer

[lechristophe]

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

[ctrueden]

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: http://www.nabble.com/macro-using-LOCI-Bio-Formats-Importer-tf4245158.html#a12080524
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[lechristophe]

Dear Curtis,

In fact, I would like to be able use Bio-Formats to detect the names of different series in a Leica LIF file, before calling it sequentially to open stacks one after another. I want to automate the basic processing of Z stacks (filtering and Z-projection), without user interaction. If I open all stacks at once, I will have memory problems and sequential processing is much more elegant.

I've seen that the macro frame has been extended in the latest imageJ version, allowing plugins to register new macro functions. This could be used for Bio-Formats, by providing a limited set of macro functions such as "output a string array of series names inside the specified file" that could enhance potential macro-automated use of the plugin.

Thanks a lot for your help !

Curtis Rueden wrote

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 <[e-mail]> 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: http://www.nabble.com/macro-using-LOCI-Bio-Formats-Importer-tf4245158.html#a12080524
> Sent from the ImageJ mailing list archive at Nabble.com.
>