Dr Jano van Hemert

Science, software and scripts

Wide Field Ophthalmic Photography Image Storage SOP Classes; DICOM Supplement 173

29 Mar 2015

With a small team comprising members from different companies and representatives of the American Academy of Ophthalmology, a new supplement was delivered from conception to approval in 14 months.

Supplement 173 defines Storage SOP Classes to enable anatomically correct measurements on wide field ophthalmic photography images.
Vendors have implemented new technology that enables the acquisition of OP images using wide field fundus photography. The Ophthalmic Photography IOD does not address wide fields, varied pixel spacing, and proper measurement of a stereographic projection or other methods of projection/mapping. Since the back of the eye is approximately a concave sphere, taking a very wide field image of it introduces large errors in any attempt to measure a lesion in that image (the error is very large when using a single value for the DICOM Pixel Spacing Attribute.). Therefore, DICOM WG 9 (Ophthalmology) has determined that two new Information Object Definitions (IODs) are necessary to adequately represent wide field fundus photography.

Manufacturers of ophthalmic photographic imaging devices have been developing OP images (using a narrow field) for many years in DICOM (i.e., these SOP Classes are widely supported by the DICOM ophthalmic community). Therefore, the wide field OP image storage SOP Classes are an extension to already existing narrow field DICOM SOP Classes.

Supplement 173 PDF

DICOM Confidential

4 Mar 2014

Medical imaging acquired for clinical purposes can have several legitimate secondary uses in research projects and teaching libraries. For these uses, and when imaging is acquired directly for research, most personal data can be safely removed, but in many cases it is necessary to keep some personal data or a link with the personal data. At this moment, no commonly accepted solution exists because the amount of personal data that is required by researchers and teaching libraries varies case by case.

DICOM Confidential is an open source DICOM (Digital Imaging and Communications in Medicine) de-identification toolkit that provides the necessary flexibility to account for different de-identification requirements and does not impose a given anonymisation model. It also provides a mechanism for forwarding the anonymous output to a remote site using either SFTP (SSH File Transfer Protocol) or DICOM communications protocol. The core functionality is contained in a Java library, which we have used to develop two DICOM anonymisation applications; these are included in the toolkit: one for DICOM files contained in a folder and one for objects received via the DICOM protocol (a receiver). A separate graphical application is provided to help users in policy writing and configuration.

In the case of multicentre clinical research projects a uniform, accountable de-identification process at all the participant centres is desirable. This can be done by prior distribution of the Privacy Policy to be used or by deploying it in a web server from which DICOM Confidential can read it directly. The toolkit was deployed in a multicentre setup and the experience gained in this deployment is presented.

Get it from SourceForge

Rapid Portal Development

2 May 2013

Rapid is a cost-effective and efficient way of designing and delivering portal interfaces to tasks that require remote compute resources. The aim of Rapid is to make completing these tasks as simple as purchasing a book or booking a flight on the web.

The philosophy of Rapid is to deliver customised graphical user interfaces that enable domain specialists to achieve their tasks. These tasks make use of domain-specific applications that run on remote compute resources; a requirement which is satisfied by translating the task into one or several computational jobs to be performed on Grid and Cloud Computing infrastructures, and High-Performance Computing facilities.

Customised interfaces allow tasks to be performed without referring to terminology about the underlying computational infrastructure. Moreover, the system allows to expose particular features of applications as not to overwhelm the user.

Extracting features from travelling salesman instances

12 Feb 2012

Contains a collection of source files authored by different people that put together allows the extraction of features from travelling salesman problem instances.

See these papers for a detailed description:

  • Discovering the suitability of optimisation algorithms by learning from evolved instances (K. Smith-Miles, J.I. van Hemert), In Annals of Mathematics and Artificial Intelligence, volume 61, 2011.
  • Evolving combinatorial problem instances that are difficult to solve (J.I. van Hemert), In Evolutionary Computation, volume 14, 2006.
  • Property analysis of symmetric travelling salesman problem instances acquired through evolution (J.I. van Hemert), In Evolutionary Computation in Combinatorial Optimization (G. Raidl, J. Gottlieb, eds.), Springer, 2005.
  • Phase transition properties of clustered travelling salesman problem instances generated with evolutionary computation (J.I. van Hemert, N.B. Urquhart), In Parallel Problem Solving from Nature (Xin Yao, Edmund Burke, Jose A. Lozano, Jim Smith, Juan J. Merelo-Guervós, John A. Bullinaria, Jonathan Rowe, Peter Ti\vno Ata Kabán, Hans-Paul Schwefel, eds.), Springer, volume 3242, 2004.


20 May 2006

This library implements a framework for an evolutionary algorithm. It aims at including different techniques from the area of evolutionary computation, such as genetic algorithms and genetic programming, in one framework. It is setup such that new projects can be implemented by adjusting only the necessary parts in the library.

Get it from SourceForge or download below.


Revisions: problems with latex-3 fixed, allmusic options works again, some new templates, new option template_list.

Dynamic Vehicle Routing Problem Generator

26 Feb 2006


This problem generator for dynamic routing problems can be used to study different aspects of real-time routing by changing parameters of the problem. It is written in Perl and has extensive documentation.