problem using LOCI tools in macro

[Aryeh Weiss]

I am using the macro extensions of bioformats, like this:

run("Bio-Formats Macro Extensions");
path = File.openDialog("Click on any image");
Ext.openImagePlus(path);

This works fine, but I cannot figure out how to set the various options
that I normally have (eg split channels, grayscale. etc).
I looked through the various macro extension commands, but I could nto
find this.

I must be missing something obvious, but I would greatly appreciate any
help. Also, a pointer to where I should have found this info would be
appreciated.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[Nathaniel Ryckman]

Here's the deal. If you want to stick with Macro language program, then you will just have to settle for missing functionality and occasional bugs.

The plugins that are created for imageJ are created by 3rd party sources. If you can't find documentation on the 3rd party websites, then the functionality that you are looking for probably doesn't exist.

Here is bio-formats website:

http://www.loci.wisc.edu/bio-formats/imagej

SOLUTION:

Learn how to create a plugin or find a better plugin.

Aryeh Weiss wrote

I am using the macro extensions of bioformats, like this:

run("Bio-Formats Macro Extensions");
path = File.openDialog("Click on any image");
Ext.openImagePlus(path);

This works fine, but I cannot figure out how to set the various options
that I normally have (eg split channels, grayscale. etc).
I looked through the various macro extension commands, but I could nto
find this.

I must be missing something obvious, but I would greatly appreciate any
help. Also, a pointer to where I should have found this info would be
appreciated.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[Martin Höhne]

Aryeh,

open a file with the LOCI-Bioformats importer while the macro recorder is running. This will show how to use the command in a macro.

I got this when selecting grayscale and split channels:

run("Bio-Formats Importer", "open=[D:\\science\\slice1.lsm] color_mode=Grayscale split_channels view=Hyperstack stack_order=XYCZT");

Hope that helps,
Martin

[Aryeh Weiss]

On 6/28/11 6:14 PM, Martin Höhne wrote:

> Aryeh,
>
> open a file with the LOCI-Bioformats importer while the macro recorder is
> running. This will show how to use the command in a macro.
>
> I got this when selecting grayscale and split channels:
>
> run("Bio-Formats Importer", "open=[D:\\science\\slice1.lsm]
> color_mode=Grayscale split_channels view=Hyperstack stack_order=XYCZT");
>

Thank you for your reply. This works. When I saw the macro extensions, I
assumed that it had to done through them, but I see that I was wrong.

I wonder if the macro extensions allow setting of these options.

Regards,
--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[ctrueden]

Hi Aryeh,

I wonder if the macro extensions allow setting of these options.
>

Fairly recently, we updated the Bio-Formats Importer API to be more
powerful. From Java or a Java-based scripting language such as Javascript or
Beanshell, you can now write:

  import loci.plugins.BF;
  ...
  ImagePlus[] imps = BF.openImagePlus("/path/to/myfile");
  for (ImagePlus imp : imps) imp.show();

This will open the given file using the default options, and display all
resultant ImagePlus objects. Or if you want to configure the options
yourself, you can write:

  import loci.plugins.BF;
  import loci.plugins.in.ImporterOptions;
  ...
  ImporterOptions options = new ImporterOptions();
  options.setId("/path/to/myfile");
  options.setCrop(true);
  options.setCropRegion(0, new Region(0, 0, 100, 120));
  options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE);
  //...etc.
  ImagePlus[] imps = BF.openImagePlus(options);
  for (ImagePlus imp : imps) imp.show();

This should work from many of Fiji's scripting languages that utilize the
Java API. However, apart from the openImagePlus(String) method with default
settings, we have not updated the Bio-Formats macro extensions to support
this API in the ImageJ macro language.

-Curtis

On Tue, Jun 28, 2011 at 11:20 AM, Aryeh Weiss <[hidden email]> wrote:

> On 6/28/11 6:14 PM, Martin Höhne wrote:
>
>> Aryeh,
>>
>> open a file with the LOCI-Bioformats importer while the macro recorder is
>> running. This will show how to use the command in a macro.
>>
>> I got this when selecting grayscale and split channels:
>>
>> run("Bio-Formats Importer", "open=[D:\\science\\slice1.**lsm]
>> color_mode=Grayscale split_channels view=Hyperstack stack_order=XYCZT");
>>
>>
> Thank you for your reply. This works. When I saw the macro extensions, I
> assumed that it had to done through them, but I see that I was wrong.
>
> I wonder if the macro extensions allow setting of these options.
>
> Regards,
>
> --aryeh
> --
> Aryeh Weiss
> School of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>