Open Microscopy Environment

Hello together.

I'm trying to write a simple ImageJ plugin. This plugin should get a NDPI file as parameter and then should save the different magnification steps in different tiff files. I have read a lot about bioformats and I'm pretty sure this could be done. But I don't know how. Since the files are very large on the higher magnifications I don't want to open them. I tried the bioformats ImageJ plugin and I could read the file and then I get a nice little preview image to all magnifications. But then the bioformats plugin wants to open the files. But it does not work because the images have a size of about 10 GByte on the highest resolution. My problem is: how to program this with the help of the bioformats library.

1. Open dialog and select ndpi file - I have done that
2. Save different magnification steps in different tiff files without opening them - Not done

If someone could help me with step number 2 that would be nice. A small code snippet or something like that would be great too.

Regards,
Eric

Hi Eric,

2. Save different magnification steps in different tiff files without opening them - Not done

If someone could help me with step number 2 that would be nice. A small code snippet or something like that would be great too.

This class is probably the closest to what you want, with the caveat that it is a command line tool and not a plugin:

https://github.com/openmicroscopy/biofo ... erter.java

You may be able to call the 'testConvert' method directly; otherwise, you should be able to adapt that code (especially 'convertTilePlane') to convert large images without having them be displayed in ImageJ.

For more concise snippets, see also:

http://www.openmicroscopy.org/site/supp ... xport.html

and especially:

http://www.openmicroscopy.org/site/supp ... rge-images

Regards,
-Melissa