Bio-Formats release (2006 Oct 27)

[ctrueden]

Hi,

Today LOCI has released a new version of Bio-Formats. Major changes include:

* Multi-series support for Slidebook
* Added support for Alicona AL3D
* Fixed plane ordering issue with FV1000 OIB
* Enhanced dimension detection in FV1000 OIF
* Added preliminary support for reading NEF images
* Added option to ignore color tables
* Fixed ImageJ GUI problems
* Fixed spatial calibration problem in ImageJ
* Fixed some lingering bugs in Zeiss ZVI support
* Fixed bugs in OME-XML reader
* Tweaked ICS floating-point logic
* Fixed memory leaks in all readers
* Better file stitching logic

You can download the release from the Bio-Formats web site:
    http://www.loci.wisc.edu/ome/formats.html

This release simplifies installation by bundling everything into a
single file, loci_tools.jar. Just drop it into your ImageJ plugins
folder, and all LOCI plugins should work. (But please delete any old
Bio-Formats JAR files -- loci_plugins.jar, bio-formats.jar,
commons-logging.jar, commons-httpclient-2.0-rc2.jar, forms-1.0.4.jar,
ome-java.jar, poi-loci.jar, xmlrpc-1.2-b1.jar -- or else there will be
problems.)

The next release will have support for Imaris 5 (TIFF variant) as well
as better NEF support.

We have also written the first draft of a "getting started" guide for
developers who wish to create additional format readers for
Bio-Formats. You can find the guide online at:
    http://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/getting-started.txt

As always, please let me know if you have any issues or questions
about the software.

Cheers,
Curtis

[Justin McGrath]

Hi Curtis,
I have .zvi images I'd like to use in ImageJ.  The images only have 2
channels taken with a black and white camera, but I have one channel
with false color.  The Bio-Formats plugin opens the files fine, but if
I select "Merge to RGB" it creates a composite with the wrong colors.
Is there a way to get the plugin to display the colors correctly?

Thanks,
Justin

On 10/27/06, Curtis Rueden <[hidden email]> wrote:

> Hi,
>
> Today LOCI has released a new version of Bio-Formats. Major changes include:
>
> * Multi-series support for Slidebook
> * Added support for Alicona AL3D
> * Fixed plane ordering issue with FV1000 OIB
> * Enhanced dimension detection in FV1000 OIF
> * Added preliminary support for reading NEF images
> * Added option to ignore color tables
> * Fixed ImageJ GUI problems
> * Fixed spatial calibration problem in ImageJ
> * Fixed some lingering bugs in Zeiss ZVI support
> * Fixed bugs in OME-XML reader
> * Tweaked ICS floating-point logic
> * Fixed memory leaks in all readers
> * Better file stitching logic
>
> You can download the release from the Bio-Formats web site:
>     http://www.loci.wisc.edu/ome/formats.html
>
> This release simplifies installation by bundling everything into a
> single file, loci_tools.jar. Just drop it into your ImageJ plugins
> folder, and all LOCI plugins should work. (But please delete any old
> Bio-Formats JAR files -- loci_plugins.jar, bio-formats.jar,
> commons-logging.jar, commons-httpclient-2.0-rc2.jar, forms-1.0.4.jar,
> ome-java.jar, poi-loci.jar, xmlrpc-1.2-b1.jar -- or else there will be
> problems.)
>
> The next release will have support for Imaris 5 (TIFF variant) as well
> as better NEF support.
>
> We have also written the first draft of a "getting started" guide for
> developers who wish to create additional format readers for
> Bio-Formats. You can find the guide online at:
>     http://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/getting-started.txt
>
> As always, please let me know if you have any issues or questions
> about the software.
>
> Cheers,
> Curtis
>

[ctrueden]

Hi Justin,

We are still ironing out the "Merge channels to RGB" option. It is
tricky for a number of reasons -- e.g., for 16-bit color data,
linearly scaling 0-65535 down to 0-255 results in nearly all pixels
appearing black for many common datasets. ImageJ solves this problem
by autoscaling the color ranges for 16-bit data. But autoscaling
requires a priori knowledge of all pixel values, which most formats do
not provide (without scanning through all the pixels).

For now, one way you can merge the colors properly is to uncheck
"Merge channels to RGB" and instead check "Open each channel in its
own window." Once the data has been imported, choose Image -> Color ->
RGB Merge... from the menu. The channels should be listed under the
appropriate components by default; if not, adjust them. Click OK, and
you'll have a merged, autoscaled image. The main dowside to this
technique is that it requires more intermediate RAM.

Please let me know if this method does not work for your data.

Thanks,
Curtis

On 10/28/06, Justin McGrath <[hidden email]> wrote:

> Hi Curtis,
> I have .zvi images I'd like to use in ImageJ.  The images only have 2
> channels taken with a black and white camera, but I have one channel
> with false color.  The Bio-Formats plugin opens the files fine, but if
> I select "Merge to RGB" it creates a composite with the wrong colors.
> Is there a way to get the plugin to display the colors correctly?
>
> Thanks,
> Justin
>
> On 10/27/06, Curtis Rueden <[hidden email]> wrote:
> > Hi,
> >
> > Today LOCI has released a new version of Bio-Formats. Major changes include:
> >
> > * Multi-series support for Slidebook
> > * Added support for Alicona AL3D
> > * Fixed plane ordering issue with FV1000 OIB
> > * Enhanced dimension detection in FV1000 OIF
> > * Added preliminary support for reading NEF images
> > * Added option to ignore color tables
> > * Fixed ImageJ GUI problems
> > * Fixed spatial calibration problem in ImageJ
> > * Fixed some lingering bugs in Zeiss ZVI support
> > * Fixed bugs in OME-XML reader
> > * Tweaked ICS floating-point logic
> > * Fixed memory leaks in all readers
> > * Better file stitching logic
> >
> > You can download the release from the Bio-Formats web site:
> >     http://www.loci.wisc.edu/ome/formats.html
> >
> > This release simplifies installation by bundling everything into a
> > single file, loci_tools.jar. Just drop it into your ImageJ plugins
> > folder, and all LOCI plugins should work. (But please delete any old
> > Bio-Formats JAR files -- loci_plugins.jar, bio-formats.jar,
> > commons-logging.jar, commons-httpclient-2.0-rc2.jar, forms-1.0.4.jar,
> > ome-java.jar, poi-loci.jar, xmlrpc-1.2-b1.jar -- or else there will be
> > problems.)
> >
> > The next release will have support for Imaris 5 (TIFF variant) as well
> > as better NEF support.
> >
> > We have also written the first draft of a "getting started" guide for
> > developers who wish to create additional format readers for
> > Bio-Formats. You can find the guide online at:
> >     http://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/getting-started.txt
> >
> > As always, please let me know if you have any issues or questions
> > about the software.
> >
> > Cheers,
> > Curtis