IIPImage is now an official Ubuntu and Debian package! Version 0.9.9 of the IIPImage server is now distributed as part of the Ubuntu 12.10 Quantal Quetzal release.  It is also included in Debian’s Sid unstable branch, and testing branch from where it should migrate to become part of the forth-coming Debian 7 Wheezy release.

The Debian source package is available here: http://packages.debian.org/source/sid/iipimage and the Ubuntu lauchpad package here: https://launchpad.net/ubuntu/+source/iipimage

The package is split into two with a main server package: iipimage-server and a separate IIPImage documentation package: iipimage-doc

So, installing IIPImage is now extremely easy. To do so on Ubuntu 12.10, simply install iipimage-server via the graphical package manager or via the command line:

apt-get install iipimage-server

and optionally for the documentation:

apt-get install iipimage-doc

Now restart Apache and you should have the IIPImage server running on http://your.server/iipsrv/iipsrv.fcgi

Only the server is included in this package, so you will need to install a client, such as IIPMooViewer or IIPZoom yourself. Note that the server URL is /iipsrv/iipsrv.fcgi and not the usual /fcgi-bin/iipsrv.fcgi, so don’t forget to set this correctly in the viewer configuration of IIPMooViewer, IIPZoom or whichever viewer you choose to use.

The package is configured to work with both Apache and Lighttpd. If you are using Apache, the configuration file is at /etc/apache2/mods-available/iipsrv.conf. For Lighttpd, /etc/lighttpd/conf-available/20-iipsrv.conf. See the server documentation page for details of the available parameters. The log file is at /var/log/iipsrv.log.

The package has Memcached support built in and will automatically use Memcached for caching if this is running on the host machine. If not, simply start it to allow IIPImage to use it.

To install on the current Debian, you will need to be on the testing (or unstable branch). If you are on testing, add an additional unstable source to /etc/apt/sources.list. See the testing documentation for further details. Make sure you first update your package index, then simply install as above.

If you want JPEG2000 support or don’t want to use the Debian testing or unstable branch, continue to use our stable but “unofficial” 0.9.9 Ubuntu packages that are compatible with Ubuntu 11.10 and 12.04.

Special thanks to Mathieu Malaterre for building and maintaining the official Debian package!

The latest development code for iipsrv, the IIPImage server is now hosted on Github. This should make things far easier for developers to share code and to submit patches. You can check out the repository here https://github.com/ruven/iipsrv

The latest code has a host of new features including:

• Exact export resizing for both TIFF and JPEG2000
• Improved interpolation algorithms for CVT export
• Extended support for 1, 8, 16 and 32 bit images
• Gamma support
• Improved metadata handling
• Performance improvements
• Improved Windows compatibility
• Bug fixes!

So, check it out and get forking!

The Leiden University Medical Centre in The Netherlands conducts a wide range of scientific research ranging from pure fundamental medical research to applied clinical research. Recently, our group in the Department of Molecular Cell Biology, published a paper entitled Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps in the Journal of Cell Biology about a pipeline to acquire, combine and visualize electron microscopy images as panoramas of virtually unlimited size. The technique, named Virtual Nanoscopy, can reveal large macromolecules, organelles, cells, tissue, up to entire animal cross-sections.

Virtual slide of a sagittal section of a Zebrafish, imaged at 1.6 nm/pixel resolution over an area of 1.5 x 0.6 mm²

As a proof of principle we have put online a 281 gigapixel ultrastructural map of a 5 days old zebrafish embryo, which is a commonly used vertebrate model organism. The virtual slide was recorded at 120 kV with a magnification at the detector plane of 9460. A total of 26,434 unbinned 4k × 4k images was collected with a FEI Eagle CCD camera (>8 s readout time full frame) in 4.5 d. The sample was maintained at −1 µm defocus throughout the whole data collection. The resulting slide of 1,461 × 604 µm² in size consists of 921,600 × 380,928 pixels of 1.6 nm square each.

The image shows the cartilage in slate blue, the eye in sienna, the brain in forest green, the muscles in salmon pink, the liver in indian red, the intestine in dark khaki, the pancreas in plum, the pronephric duct in yellow, the olfactory pit in lime green and the yolk in turquoise. Other examples can be found in the data section of our website.

Virtual nanoscopy has changed the way electron microscopy is carried out in our laboratory. Instead of collecting just a snapshot of part of a cell, we now routinely collect entire cross-sections which provides a much better context of the observed phenomena. Afterwards the data can be browsed as if behind a microscope at nanometer scale, hence the name virtual nanoscopy.

To visualise these images on the web we use the IIPImage server in combination with IIPMooviewer, both of which we adapted slightly to our needs. The images are stored as TIFF tiled image pyramids using the BigTIFF extensions available in libtiff 4.0 with a tile size of 256×256 pixels.

We can only recommend IIPImage and greatly appreciate the quick feedback from the developers. Many thanks to the developers of IIPImage for sharing their creation with the world!

by Frank Faas & Raimond Ravelli, Department of Molecular Cell Biology, Leiden University Medical Center

The proliferation of mobile devices has made responsive web design one of the hottest topics in web design. Modern web sites need to be usable on a large range of screen resolutions and sizes, from low resolution mobile devices to high resolution monitors. For page layout, various techniques based on fluid layouts, media-queries or combinations of these with HTML5 have been developed, which adapt layout to suit the available screen size.

Responsive Images

However, images themselves also need to adapt to the context, not just for maintaining layout, but also to reduce unnecessary bandwidth. The solve this, the concept of responsive images (or adaptive images) enables the browser to request an image at a size appropriate for the screen resolution. A number of possible solutions have been put forward via the W3C’s Responsive Images Community Group and elsewhere.

Read the rest…

Version 0.2 of our analytics tool, IIPAnalyze is now available! This version adds user agent filtering as well as histograms showing user activity over time. The following histograms, for example, show how the frequency of tile requests made (by all users and only Firefox users) varies with time after the users first load the IIPImage viewer for our Marble Earth demo.

Frequency of Tile Requests over Time for Marble Earth by Firefox Users

Tile Request Frequency for Marble Earth by all Users over First 2 Minutes

It is also possible to just look at just one particular user and how their tile requests vary with time. This is the request pattern of a random IP address viewing the Marble Earth IIPImage demo showing the first minute or so of activity.

Tile Request Frequency for a Random IP address

See the analytics documentation page for more information and the list of options. You can download the latest stable release of IIPAnalyze from our download page or fork the latest development code from the iipanalyze github repository.

Thanks once again to Laurent Le Guen for the updated script.