New 3D software


3DSteriod an Android App version of StereoPhoto Maker by Masuji Suto

iPhone version i3DSteroid.

A new version of StereoPhoto Maker has recently been made available.


Celebrations at Royal Geographical Society – as awarded SSI links to EPSRC UK-USA collaboration

Over 2017 the CCPi ( had an active round of networking and outreach meetings for X-ray CT, culminating with a recognition dinner held at the Royal Geographical Society.


In the start of 2017 we provided a Letter of Support for a DOE project proposed by Kitware inc., as well as submitted our own CCP Flagship proposal. Both were awarded, creating an extra 6 FTE RSE in the UK and 5.1 FTE RSE (Research Software Engineers) in the USA until 2020.
Following this success we were left with a concern that there were no face-to-face networking funds, but alternative electronic systems were being considered until serendipity! – the EPSRC launched a grant with the support of the SSI (Software Sustainability Institute), to ask for travel and subsistence to foster collaborations between research software engineers on both sides of the pond. We applied and had a two week face-to-face collaboration with one of the main Kitware Inc. lead developers, Dr Marcus Hanwell. The topics focussed on their new Tomviz software product ( a purpose built open source application that can manage – the data collection; noise filtering, reconstruction, visualisation and final analysis of tomography data.

Talks, facility tours (university labs, ISIS (IMAT) and Diamond (i13) beamlines) and software installation sessions occurred, at RAL (Atlas Visualisation Facility), DL (Hartree Centre visualisation suite) and the University of Manchester (HMXIF) and were enabled by the current extensive CCPi network.


The CCPi now has a presence at three major annual imaging events in the country; each having 50+ attendees. These include an X-Ray user group symposium (ToScA) managed by the National History Museum (NHM) and Royal Microscopical Society (RMS), a technical forum supported by RCaH and DLS; and a “dimensional XCT” conference supported by NPL that is leading to formal BSI/ISO standards.


In 2018, for this UK-USA collaboration, we are looking at new user guides to be created, an open day for software show-and-tell event at RAL and further direct collaboration between the newly recruited software developers to share code and best practice; as well as links to other CCPs involving tomography type data. A follow on impact showcase event will be organised under the EPSRC RSE & ARCHER umbrella on Tuesday 24 April 2018.

TB Visualisation

In the UK there are some medium sized HPC systems being installed, funded by the Research Councils. The tier 2 HPC launch event on 30 March 2017 – and made announcements by the EPSRC CEO Philip Nelson and from Susan Morell (Birmingham)
Peter Vincent (Imperial) presented the PyFR higher-order polynomial CFD that works on all architectures -giving 13.7 petaflops on the USA Titan system. He described VTKm for remote visualisation that rendered the 1TB per-frame data in-situ -vis:
… this claimed and showed you could stream video sets from the 1TB data file stored in the HPC memory in this virtual wind-tunnel type simulation, without saving the data first (or importantly moving it anywhere). it used a type of Catalyst within kitware’s range of tools so could produce paraview type effects.
The results are very impressive, and similar systems are being used in other remote projects. It does require:
  • knowledge of what you wish to view before you compute
  • unable – or difficult – to change the visualisation results (sub-parameters)
  • unknown question as to if you should (or can) store the intermediate data – would take many minutes or longer to do this.
  • cost of visualisation is include – or added to – the cost of HPC so needs accounting for.


Materials Science Regius Professor Celebration

My kind of desk – pre-work within Research IT office, for a touchtable and projection display stand at the University of Manchester Regius Professorship award celebration.

Using the new Acer Predator (17 G9-792) laptop, with an inbuilt great graphics card (NVIDIA® GeForce® GTX 970M with 6GB GDDR5 Dedicated Memory), and touchscreen – bits borrowed from UoM and STFC visualisation groups along with (STFC tomography data and the drishti-prayog volume visualisation software all appear to run extremely sweet.WP_20170411_001_cMoving this to the exhibition area within the NGI (National Graphine Institute) with a HDMI splitter should then be suitable for 100’s of viewers per hour …

Show setup for 150+ special visitors. This example on the screen (one of about 15), just prepared, showed work from by the new EPSRC Flagship CCPi fellowship, Daniil Kazantsev et al from RAL that using multiple volume vis transfer functions highlighted the centre and the fractal edge of slices showing dendritic behaviour (even measurable).


The laptop and small workstation were hidden and all you see is the touchtable, controlled by the operator or user on the right, and the main screen allowing multiple people to view and comment at once.

The volume visualisation was a little tricky as the raw data had been pre-segmented already so I had to create a boundary edge by interpolation and reducing the size of the complete object.

There was a talk by Regius Phil Withers after a presentation of the award from the Queen’s representative, as well as a question and answer session chaired by the President of the University of Manchester.

Old fashioned video streams

Not really vis but this was important in the day.

Back in the Computer Lab., at the University of Cambridge in about 1992 there were at least two filter coffee systems; both running on a slow drip-filter setup. The Rainbow Group had access to one machine in a walk down a corridor to a small kitchenette; but the network team had to travel a lot longer way to their coffee machine. A problem of lack of enthusiasm to travel meant that often they would find an empty coffee pot – or even worse stale coffee. A solution was a camera video stream that linked to the linux server and stream images to X Windows. So when new fresh coffee arrived this would be obvious from the image on everyone’s desktop. have been rebuilding old systems and in East London they rebuild the Cambridge Coffee pot scenario – with similar equipment. There is a wikipedia page on the original:


Is video streaming – visualisation – well definitely yes as it is an interpretation. Due to low quality network speed and CPUs; the small 128×128 video stream of images had to just include the coffee level and also the fps was about one frame every few seconds – but that is a good rate and good enough resolution for “coffee pot observation”.

Touching …. vol vis …

Touchscreens are all the fashion – but  any system you deploy is expected to work smoothly and intuitively – including visualisation ones. There are some company purpose-built systems for exhibitions that are far from cheap although they may work well they can also suffer from lack of agility when recreate new content. There are also simple tablet/phone software options available for touching and manipulating volumes but can have limited graphics ability.

Over the last couple of years we have collaborated informally with partners to share knowledge on open source solutions for large scale volume visualisation (say greater than 256 x 256 x 256) on a touchscreen device.

A hardware specification service has evolved where we can assist with advice and quotes for touchscreen and workstation visualisation nodes, as well as more importantly related software installation; used for exhibitions and PE. A wiki is available at:

At Manchester, connecting through Research IT, there are now groups available to informally share equipment and expertise – and as importantly share experience in interacting with the public and other scientists – even if their research data content is often diversely different.

  • MRI medical data e.g. exploring white-matter changes within the human brain: Geoff J M Parker, Hamied Haroom, Saray Parkes (ISBE)
  • Multiple Materials Science analysis e.g. cracks, fibres and mechanical defects: Sarah-Jane Clelland, Phil Withers (MXIF)
  • Fossil and everything ancient within the Manchester Museum: Russell Garwood, Alan Brown, Campbell Price, Roy Wogelius (ICAL)

Both being asked to be available for the upcoming Presidents Office organised ‘University Celebrations of Regius Professorship’ on 25 April 2017 in the NGI.