IC3D (preparation)

The big brilliant news this week is that I have been accepted to present some of my data at IC3D this year in Liege! It’s an international conference focussing mostly on my field of interest and it is a peer reviewed conference so the kudos is rather high!

They have taken my paper on oblique viewing angles nicely and want me to present it. They have returned the paper with some reviewer comments for minor alterations, which I am currently working with Jenny to get done. However one of the comments was, quite simply, to remove some of the irrelevant pieces of information I provide. I think this is in itself a bit of an annoying thing to say, because as a scientist, and a mathematician, I really try to only say the important stuff! If life could be bullet pointed that would suit me to a tee.

So I am now in the process of sorting out the paper, and also being sure I can publish the full study still in a good journal (hopefully Journal of Vision), before the deadline of a week on Wednesday.

Time flies when you’re having fun, I can’t believe it’s already November of this year! I would advocate anybody who likes hard, ever-changing and challenging work to go into research. I’m certainly living the dream!

British Science Festival

This has been an exceptionally good and fun week doing the British Science Festival. Lisa had set up a workshop all on camouflage and mimicry and during all the lab helped out (although kudos to Lisa who managed to do every session with a big smile on her face!). There were lots of different activities to do during the workshop including a load of real life creepy crawlies that were all experts at camouflage. My task was to take the children through some posters and do some questions on a quiz sheet. The first question was to do with mimicry. I explained that a hoverfly pretends to be a wasp so that it doesn’t get eaten by birds and we had three example hoverflies from different species trying to mimic a wasp. The children had to rank them in order of ‘most waspishness’ and everybody agreed one was rubbish, one was good, and one was OK. They found it very interesting that birds actually saw our OK mimic as a good mimic and our good mimic as an OK one, and some even ventured a guess that it meant birds see things differently from ours.

Next up on the quiz was aposematism. For those that don’t know, aposematism is the act of being very bright and colourful to warn predators away from eating them, we had examples such as a bee (black and yellow, ‘I’ve got a stinger leave me alone’), a poison arrow frog (Black and yellow patterns ‘don’t eat me I’m poisonous’) and the bombardier beetle (red and black ‘don’t eat me or I’ll spray you with a horrible stink, the kids particularly loved this one!). As a group we then discussed other aposmatic creatures. I had some very interesting answers, of which most were brightly coloured but more to stay camouflaged (tiger, zebra and clown fish). I had some that were mimics or dangerous in their own way (milk snake and sea anemone) and some really good answers (ladybird, skunk, wasp, ringed octopus).

The final two questions involved matching the creature to the type of camouflage it was using, and then guessing which out of 14 butterflies were poisonous and tasty. After the quiz was finished the kids rotated and did something else in the room (which you will probably hear about in other blog posts) and I started again with the next group.

The entire workshop was a great success and I really think some kids took some real knowledge and interest away from the day, and I heard more than one say it had been the best one they had seen yet. Very pleased I volunteered to help out with the event!

Tying up some loose ends

While I wait to begin construction of my next experiment (assessment panel approval pending) I have been working hard on various different bits and pieces. My paper for the oblique angles study is almost ready for submission (bar the inevitable red pen from Jenny, and a results section that is still half-written as we finish analysing the results) and I am pleased with the progress. With the analysis we have constructed various models to try to map the data, with my personal favourite being a combination of two Gaussian curves, and others including absolute values (which means the magnitude of the number only, not the sign, for example the absolute value of -2 is just 2) and polynomials (terms with powers, such as squared and cubed etc.).

Jenny and I are discussing these later this week, to decide which is the best to model the data. We have assessed the significance using SPSS already so all we really want is a nice smooth model to represent the data well. I am thrilled to announce we do have significant results however, which is something scientists always like to hear! While I don’t agree with the practice it seems to me a trend in journals is that significant results get published much more. Probably because significance proves something, where a lack of significance, by definition, proves nothing.

For example if you spin a 5 coloured spinner and say ‘it is definitely red’ – then you have a result (red). However if you say ‘it is not definitely red’ you cannot say anything about the results. It may in fact be red. But even if it is not you have no idea what colour it really is.

I can see the argument for such papers (definitely red) getting preference but I do believe scientific research would develop much quicker were all the non-significant tests and results published, even somewhere open access like wikipedia. If only to check nobody has already tried what you’re thinking of and failing. Such a site may indeed exist but I haven’t heard of it. Some non-significant result papers do make it in if they are well written or have original methodology, but the habit of selecting significant papers is one I think sometimes hinders scientific development. Just my opinion.

Wow got a bit sidetracked there! So while waiting for my next experiment to be approved and set up I have also submitted my paper on oblique angles to IC3D to see if they would like me to present (still waiting to hear from them) and I am presenting a poster twice in the space of a week! Once at an internal ION event (postgraduate poster evening, should be fun) and NEPG2013 (6-university wide event where postgrads can submit, and I was selected. Much more formal and a bigger deal!) So I am looking forward to that.

Lastly I have assembled my team of supervisors properly for my PhD. Tom Smulders, who did animal behaviour with me in my MRES year, and Vivek Nityananda, a member of the lab, will join Jenny in making sure my PhD goes without a hiccup!

British science festival, modelling and good time management

It is the British Science Festival (known from here as BSF) next week in Newcastle so the institute is very bustly over the last few days. Lisa on our team has done a tremendous job of organising not 1, not 2, but three timetables and stands for the BSF for our lab and affiliates to run. I’m heading up the poster and worksheet team, and hence working on it every day next week when it is on (mon – thurs). So if anybody does want to come and see the brilliance that is pure science and learn something new, come on down! I’ll be the guy with a big smile getting far too into the role.

In amongst that this week I have started the task of juggling my PhD. I say and really mean juggle, as even though I am only one month into a 36 month process I currently have two papers on the go, a mathematical modelling code to simplify, a student (Pramod) to keep an eye on for a long term piece, an online survey to collect data, a journal club to attend and various other equally important but not massively time consuming things to consider. Anybody who wants to get into science needs to have the focus and attention to concentrate on one problem for weeks on end, but also the ability to chop and change quickly between jobs and problems. How my supervisor Jenny copes is beyond me, as she (being the PI) is juggling the jugglers! that’s like juggling squared!

The modelling is taking up a lot of my time. The oblique angle study that I did for my MRES needs some statistical analysis before we can submit it to Journal of Vision, and that involves a lot of complex mathematical conversations with Jenny, something I properly enjoy! It does also require some serious matlab and more than a little bit of concentration. We have two normal (or Gaussian curves) centred around perpendicular viewing, and also on the angle for which the person is actually sat at, and we weigh the two curves accordingly, then optimise to fit the data. This is both very finicky (exact character matching and just missing a colon or a bracket brings everything falling apart) and time consuming. However it has been fun and the end is in sight. We have two options to pursue: an addition of the weighted curves or a multiplication. Looking at the fitted models in the graphs to me it appears that the addition route will give us a better fit. We then test this using bootstrap resampling (take all the data we collected, put it all together and mix it up, pick some data and random and go again) to determine how well the fit really is quantitatively.

Next week is all BSF, and hopefully a little bit of advancement on a paper on illusions I have written for the Leicester conference.

Dissertation deadline looming

Over the past few weeks all my work has been focussed on one thing and one thing only: The looming deadline for my 7500 word dissertation on the research I have done over the past 7 months. I finally submitted it yesterday after a bit of back and forth between Jenny and myself with advice on what to chop and change and then after some formatting / binding issues (why double spaced? It uses unnecessary paper and looks worse!) submitted it both online via the NESS internal system and handed in two hard copies to the graduate school. This week I have also submitted an abstract to a conference in America (SMPTE) and have helped out with an outreach activity:

Some of the less well represented schools and colleges in the area brought their students to the university to give them a glimpse at university life to try and encourage them to go along. Because Newcastle doesn’t have a neuroscience undergraduate course the ION set up a stall/desk next to the boardroom where the talks were taking place after a talk on psychology – neuroscience PhD. Then any interested students came to talk to us about questions they had about life as a PhD student and what studying neuroscience was like and how to get into it. I thought I was well placed to talk to people about it because I’m actually mathematically backgrounded rather than psychology, biology or chemistry. Quite a number of students came to ask questions during the hour and I thought it was certainly a help to the students!

Now that the dissertation is submitted I am looking at submitting the work as a paper to a journal (hopefully Journal of Vision, or something similar) and working on another paper regarding the illusions at the Leicester conference I went to, as well as working on a presentation for the final aspect of my MRES year. The beginning of my PhD is nearly here and I’m very excited to get straight into it!

Data collection

This week I have been working very hard at data collection. Getting the cubes (which we managed to get correctly aligned last week) into a workable experiment program took some debugging but we got it sorted shortly after the Leicester conference. Since then 9 participants have come in to take part in the experiment and the data so far looks good. The conference in Leicester went very well. I was well received, the audience seemed engaged and asked questions and a coulpe of neuroscientists in the crowd caught up with me later to bash heads on ideas that I may/could use for my PhD. Jenny has asked me to start thinking about what it is that I wish to look at and I have a few ideas, most of them relating to comfort (and therefore discomfort) while watching 3D TV. The program on the laptop was a huge hit and everybody wanted to have a go!

My deadline for the dissertation and presentation/poster/abstract are beginning to get closer so the next few weeks I will be working on statistically analysing my data, organising my work and writing it up. I am presenting for the behaviour staff next Thursday and that will be my most pressing subject to handle over the weekend.

OpenGL and NEPG

Last weeks debugging finally came to fruition on Friday, with Jenny and myself knocking our brains together for the past 3 days and coming up with the solution to the problem. After altering the viewing frustum using some mathematics and then changing the code with loading identity matrices and rendering the texture we got a perfectly lined up, textured, solid cube in openGL which mapped perfectly onto the points already worked out previously using vector mathematics and trigonometry. So the next step (which is going to be the majority of this weeks work) is to implement it into a matlab program to allow it to be ran and the experiment to be done and recorded. Some images of the cube lined up against a perspex proof are shown here. We put the coordinates of one of the faces in at a funny angle of both rotation about the perspex and the table, calculate the coordinates in world space (in cm) and put them into the code. Open GL recreates the same points perfectly on the screen for the viewpoint. A laser was used to make sure the origin was lined up correctly on the screen (you can see the red laser crosshair on the chinrest on one of the photos) and a laser distance measurer was used to judge the distance from the screen.


This week I am also submitting an abstract to NEPG, which is the North East Postgraduate Conference, a coming together of many northern universities (from Edinburgh to Leeds) to present data and information. I hope to be given a spot to present in, or a poster place. Either way it’s an exciting prospect to hopefully present up here for my peers to see what it is that I am doing. Regardless of acceptance or not I look forward to seeing other works and attending talks.

To finish off the week I am giving a talk in Leicester on Friday titled ‘an illusion using 3D technology’. Which will be my first time presenting my data to anybody. While I am not in any way nervous yet I imagine I will be come 9:15 when I open the talks of the day as the first speaker. Wish me luck!

A week of debugging

This week has been a very varied and interesting one. I began by sorting out some acetate sheets for my perspex from which I could draw some stimulus, have them represented on the computer, and then check to see if my program was working as I intended it (see below pictures for examples of the pictures, lines and 3D cube used, I also used some random points to see if that also worked and eventually it did, not pictured). The immediate problem I could see was that the pictures were lining up perfectly fine when my angle of rotation was zero, but then if I rotated clockwise the images translated left and anticlockwise right. Because of this I realised that the centre of rotation I had organised (the centre of the television) was not in fact where the origin in my screenspace was. I adjusted the stand accordingly, by moving the television backwards, and it all worked perfectly.

After that I ran through the experiment myself for a full set of data and analysed the results, which show as I suspected that the slight translation made very little difference to the perception of the cube.

I am still working on getting the cubes working in openGL, which is becoming less painful the more I look at it, the cubes now warp and the backs can’t be seen when they shouldn’t. Still a work in progress, watch this space. The advantage I have is that the ‘extra parts’ such as turning it 3D, randomly interleaving many different variables and recording the results should be relatively straightforward as it can just be ported from phase 1.

I helped out at Kids Kabin again this week, (Ann the supervisor came to make up numbers and said my calling in life must eventually involve teaching, quite a nice compliment!) I have begun working on my dissertation with a bit more earnest (reading and re-reading appropriate papers, starting my introduction and materials and methods sections, etc.). I have also signed up to attend a conference on matlab in late June (only a week before my wedding) and have worked on my presentation at a conference in a fortnights time.

Next week I intend to continue with the openGL work, I am thinking of different ways I could present the problem in case what we are trying is physically impossible, possibly an adjustment task where the cube warps depending on the right or left keypresses, and the participant has to do it until they believe the cube is no longer warped, starting at different angles. Think that would be both feasible to program and quite interesting. Will see what Jenny thinks next week.

Slow and Steady wins the race.

I have spent the entire week battling with OpenGL. OpenGL is a graphics program that is supposed to make life easier for you by doing much of the hard calculations to project an object correctly onto the screen. Unfortunately this is the exact opposite of what it is I want to do, as I’m doing oblique angles instead of frontoparallel (straight on). The advantage that OpenGL has however is that it is very good with figuring out what should be able to be seen at any one moment. So in this program the back of my cubes aren’t visible when they shouldn’t be, which is exactly why we opted to use openGL for phase 2. Unfortunately I now need to reassess how to work out the oblique warping all over again. Fortunately I intend to use previous thinking as a ‘roadmap’ to avoid any of the pitfalls I suffered before.

I now have 7 weeks until the project is supposed to be finished. If I can get the cubes working in the next two weeks I’ll have more than enough time to run through some volunteers and collect some results. How do I know I have 7 weeks left? My wedding is the Saturday after the project is done. Which is altogether much more scary than science!

A frustrating week

This week I have been working with the problem of trying to add some solidity to my wire frame cubes via putting surfaces on them. Which sounds fairly trivial but has taken me the best part of a week to sort out. Needed to use Screen(FillPoly,…) and enter the coordinates my sph2cart(theta, phi, fancy R) returned. But this in itself raises a problem. Due to the 3D being used and the entire thing being on one plane when it is done, filling raises more problems then it solves, and the back surface can be seen on the wrong size (PTB does nothing for hidden faces, or at least not automatically)

SO it looks like I may have to write a new piece of code, using openGL. Which I would prefer to avoid as it’s a different beast altogether and will take a while. Going to look today at what I hope will be half measures to see if I can find a workaround in PTB. Not too hopeful though!

In other news I have received and setup the active stereo on my laptop. Have to say it looks brilliant and the screen quality is super HD anyway. So have been working with that and seeing if I can adapt matlab so it work in active stereo (managed it for basic matlab codes, not yet for my script). The number of volunteers I am getting from ION database is brilliant and I now have more than enough to do phase 1 and 2. Reluctant to turn any of them away in case I do need more for the power of the stats used. I have also been working on the abstract and presentation for the illusion conference in Leicester in June (excited for that).

Here are a couple of photos of the lab setup for this experiment and what the participant can see through the screen. As is clear, the curtain makes the orientation of the screen plane appear frontoparallel (perpendicular) whereas the other pictures show it is not!


How the illusion appearsBehind the curtain