On 10/7/2012 4:43 PM, Andrzej Ole? wrote:
> We are happy to announce that with Bioconductor release 2.11 the
> package EBImage (>= 4.0.0) can be installed without any of the
system
> dependencies that were required by previous versions (ImageMagick,
> GTK+).
>
> Further functionality upgrades include:
> - Perreault's constant time median filter,
> - self-complementary top-hat,
> - streamlined object feature computations,
> - improved 'rotate' / 'translate' functions and a new 'transpose'
function,
> - alpha channel support,
> - and performance enhancements.
>
> See the package NEWS file and documentation for details.
>
>
> Andrzej Oles
> EBImage Development Team
>
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It used to take forever to get GTK+ and ImageMagick installed and
working properly, so I really appreciate your new approach. However,
there is a browser-dependency with the new display() function.
> nuc = readImage(system.file('images', 'nuclei.tif',
package='EBImage'))
image 510 x 510 x 0, tiles 0 x 0, bps = 8, spp = 1 (output 1), config
=
1, colormap = no
image 510 x 510 x 0, tiles 0 x 0, bps = 8, spp = 1 (output 1), config
=
1, colormap = no
image 510 x 510 x 0, tiles 0 x 0, bps = 8, spp = 1 (output 1), config
=
1, colormap = no
image 510 x 510 x 0, tiles 0 x 0, bps = 8, spp = 1 (output 1), config
=
1, colormap = no
> display(nuc)
On Windows 7 64-bit with IE 9.0 as my default browser, I get the
browser
starting with the message, "Internet Explorer restricted this web page
from running scripts or ActiveX controls". If I click the
button,"Allow
Blocked Content", I still get no display of the images. The display
command therefore appears to fail. If I do to use the built-in raster
display:
display(nuc, method = 'raster'),
or better, display(nuc, method = 'raster', all = TRUE)
the images display quite nicely.
I'm not quite sure why you picked "browser-based display" as the
default, but it seems there should be checking to see if the
appropriate
browser controls are available if the browser display is to be the
default. Just for completeness, if Chrome (my more common default
browser) or Mozilla Firefox are my defaults, the browser based display
works fine. Note here though, that I have a current and
well-functioning Java that didn't exist by default on the Windows
platform. Do you have code that should install an ActiveX control in
IE
that is not functioning properly? The issue with browser-based
display
as the default is "reliability" not "flexibility".
I do not have Safari or Opera installed on this computer so I have not
tried them.
Let me finish with a wishlist item. I would be terrific if there were
a
way to directly tie the OME data model
http://www.openmicroscopy.org/site/support/file-formats to EBImage
processing in R. Being able to deal with multidimensional data and
manage the mass of metadata associated with images seems destined to
be
the future. I know this is a BIG WISH not easily fulfilled, but I
thought I'd express it anyway.
Again, I'm grateful for what you've already contributed with the
existing EBImage! Kudos to you on a terrific package!
Rob Baer
Thanks,
Rob Baer
