[ome-users] Writing conventional TIFF through BioFormats exporter

[simon andrews]

I am writing a small application to automate the processing of some data we've generated.  The processing works fine but I've found that the TIFFs which are written my the native FileSave in ImageJ cannot be opened by the proprietary application we need to use later in the pipeline.  I've also found that TIFFs written using the BioFormats exporter do work so I want to use this instead of the ImageJ exporter.

The application I'm using uses the ImageJ API but there isn't a full ImageJ install.  I can do the export manually in ImageJ to see a macro command like this:

run("Bio-Formats Exporter", "save=[D:\\Images\\Test\\Registration\\bio_formats.tif] compression=Uncompressed");

..but I need to be able to replicate this in conventional java within my program.  I have a simple (non-stacked) ImagePlus object with the data in it and I know the location of the file I want to save.  I need a conventional (rather than OME) and uncompressed TIFF.

I've tried playing around with the options under IJ.runPlugin and with using ImageWriter directly but can't seem to make this work in my environment.  I also suspect there may be a better way to do this within the bioformats API but couldn't find an example which did this.

Can anyone suggest a small snippet of code to show how this should work please?

Many thanks

Simon.

The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902.

The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.uk<http://www.babraham.ac.uk/email_disclaimer.html>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20130617/2c9a69ea/attachment.html>