[ome-users] Can I convert 1-bit PNG files to 1-bit OME.TIFF files?

[Curtis Rueden]

Hi Frans,

Sorry for the delay in my reply, but I was waiting to discuss your question
with the other OME developers on our weekly conference call.

Is it possible to convert 1-bit PNG files (cell-boundaries as a binay image)
> to 1-bit OME.Tiff  files?
>
> If I use the bfconvert command line tool, it ends up as a UINT8 image…
>
> The (compressed) PNG file is only 4 K, the Tiff becomes 3900 K.
>
>
Yes, as you point out, right now the conversion expands the data to uint8.
We definitely want to support other bit depths, including 1-bit, 2-bit and
4-bit packed. Doing so involves adding new pixel types to the OME data
model, and making some changes to the Bio-Formats API. My current idea is to
have a flag in IFormatReader that instructs Bio-Formats whether to expand to
the nearest byte boundary -- i.e., when set, binary data would become uint8,
and when left unset, data would remain packed. This way, applications like
OMERO.importer can continue to function without needing to immediately add
support for binary data to the OMERO server, and we can also go ahead and
improve the ImageJ importer plugin to read in binary data without expansion
into ImageJ. This change, together with some improvements to the TIFF
writer, would also allow you to convert 1-bit data to OME-TIFF format.
Eventually OMERO.server could support the other types if we decide that's
the route we want to go.

Regardless, we want to provide a solution that does not take orders of
magnitude more space than necessary. We are still finalizing our plan and
will file appropriate Trac tickets soon.

I have individual  overlay files for the CellBodies, the Nuclei and the
> Neurites.
>
> Ultimately, I want to import these PNG files as new "Channels" of an
> existing file (with already 2 channels) to show it as an "overlay" in the
> Insight Viewer.
>
> Are there easier ways to do this ?
>

I also agree with Ghislain Bonamy that ultimately, it would be good to
somehow support binary images as masks within the ROI model, but that is
still a ways off.

-Curtis

On Mon, Jan 5, 2009 at 8:50 AM, Cornelissen, Frans [PRDBE] <
FCORNELI at its.jnj.com> wrote:

>
>    All,
>
>             best wishes for 2009
>
> Is it possible to convert 1-bit PNG files (cell-boundaries as a binay
> image) to 1-bit OME.Tiff  files?
>
> If I use the bfconvert command line tool, it ends up as a UINT8 image…
>
> The (compressed) PNG file is only 4 K, the Tiff becomes 3900 K.
>
> I have individual  overlay files for the CellBodies, the Nuclei and the
> Neurites.
>
> Ultimately, I want to import these PNG files as new "Channels" of an
> existing file (with already 2 channels) to show it as an "overlay" in the
> Insight Viewer.
>
> Are there easier ways to do this ?
>
> Thanks,
>
> Best regads, frans
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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