[ome-users] Writing conventional TIFF through BioFormats exporter

[Curtis Rueden]

Hi Simon,

> I need to be able to replicate this in conventional java within my
> program.

Did you try a simple conversion of the macro code using IJ.runPlugin? This
would be simpler than trying to invoke a lower-level Bio-Formats export API.

Regards,
Curtis

P.S. If you really want to get into the lower-level API, the guide is here:

https://www.openmicroscopy.org/site/support/bio-formats4/developers/export.html


On Mon, Jun 17, 2013 at 9:54 AM, simon andrews <simon.andrews at babraham.ac.uk
> wrote:

>  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.
>
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