In Rainbows


Our department recently obtained a custom-made Psychology logo rainbow flag to celebrate pride month.


This matches the rainbow seating in our staff room!


Vision in amblyopia


In recent years there have been a number of treatments proposed for amblyopia in adults. These treatments (reviewed in this paper) often involve balancing the inputs to the two eyes – down-weighting the input to the stronger eye to allow the weaker eye to contribute. The treatments improve visual function in the amblyopic eye, and some patients have even recovered stereo vision (e.g. see this TEDx video by ‘stereo’ Sue Barry). However we know very little about the mechanisms by which these improvements occur, or indeed what the nature of the neural deficits in amblyopia actually are.

Today a new paper came out online in the journal Investigative Ophthalmology & Vision Science. In it, we show that neural responses in amblyopia are reduced in the affected eye. We used a steady-state visual evoked potential technique to measure responses in each eye. The reductions are large enough that they could potentially be used to monitor improvements in visual function during treatment.

These data served as the pilot results for a grant proposal that was recently funded by the Centre for Chronic Diseases and Disorders (and part-funded by the Wellcome Trust). The plan is to use both fMRI and EEG to understand the architecture of the amblyopic binocular visual system, and to monitor improvements in visual function during a course of therapy. A postdoc job is available for 18 months to work on this project, and I’d be very interested in hearing from qualified applicants before the deadline (27th February 2015).

Welcome to new PhD students


Our term started last week. Returning to the lab is Greta Vilidaitė. Greta completed a summer project last year, and now returns as a PhD student. Her project will investigate abnormalities of neural noise in autism spectrum disorders. She is pictured here drinking some very strong mead from her native Lithuania.


Another new addition is Dave Coggan. Dave completed our Cognitive Neuroscience masters course last year, and now returns to start a PhD supervised by Tim Andrews and myself. He will study processes of mid-level vision using fMRI. He is pictured here singing at the annual ECR karaoke night.


Arduino sound to TTL trigger for EEG


A recent query on the Psychtoolbox mailing list about triggers for EEG prompted me to write an explanation of the system we developed at York to do this. I use the method below for steady state EEG, but it should work just as well for ERP designs. The arduino sound trigger was first constructed by my colleague Becky Gilbert, and she has kindly allowed me to share the design and her code.

It uses an Arduino UNO, to which we attached an audio jack socket to the analog input pin A0 (and a ground pin), and a BNC socket to the digital output pin 13. The board was mounted in a standard box. We had our technician drill holes in the box and mount the ports in it for stability. The whole thing is small (11×6.5cm), and powered from USB. Here is a picture with the lid off:


Arduino trigger

We then used the arduino software to upload a script to the board (appended below). It’s a very simple bit of code that just monitors the analog input for changes in voltage above a specific threshold. When a voltage change happens it sends a brief trigger on the digital output, at the appropriate voltage for a TTL pulse. Note that on some systems this pulse is too brief to be detected. If this occurs, inserting a brief pause (e.g. uncomment the //delay(100);) after the digitalWrite(outPin, HIGH) line will extend the pulse.

I connect the jack socket to the headphone socket of the stimulus computer, and the BNC to the trigger socket on the EEG/MEG amplifier system. I use the PsychPortAudio commands in Psychtoolbox to produce a 50ms binary pulse:

PsychPortAudio(‘FillBuffer’, tr, ones(1,220));

which I play at stimulus onset (e.g. directly after a Flip command) using:

PsychPortAudio(‘Start’, tr);

I’ve tested the arduino with an oscilloscope, and it responds within a millisecond of receiving the sound pulse. Of course, the timing accuracy of the sound pulse will depend on your computer hardware – see the PTB documentation and use PsychPortAudioTimingTest to check this. On most systems I’ve tried, the latency is very small indeed, so triggers should be completed well within one screen refresh.

I hope people find this useful, and particular credit to Becky (@BeckyAGilbert) for designing the system. If you have any problems, please leave comments below. Of course producing the box requires a some soldering, and we take no responsibility for any resulting injury, death etc. 😉



#define DEBUG 0 // change to 1 to debug 
 #define THRESHOLD 0.1 // adjust this to control sensitivity in detection of voltage increase
 const int outPin = 13; // change output (D) pin number here
 int prev_voltage = 0; // must be initialized to something
 void setup() {
  if(DEBUG) {
   // initialize serial communication at 9600 bits per second (to write debugging info back to terminal)
  // set output pin
  pinMode(outPin, OUTPUT);
 void loop() {
   // read input on analog pin 0
  int sensorValue = analogRead(A0); // change input (A) pin number here
  // convert analog reading (from 0-1023) to digital
  float voltage = sensorValue * (5.0 / 1023.0);
 if(DEBUG) {
    // print value to serial port (view in Tools > Serial Port Monitor)
    Serial.println(voltage); // This delays the trigger by
                             // about 6ms so remove before using
                             // during experiments
    // Simplest algorithm ever.  
    if (voltage > prev_voltage + THRESHOLD)
      digitalWrite(outPin, HIGH);
     digitalWrite(outPin, LOW); 
   prev_voltage = voltage;

Videos of ECVP noise symposium


A few weeks ago, at ECVP in Bremen, we held a symposium entitled “Visual noise: new insights”. The talks were varied and interesting, and have been recorded for the benefit of those who were unable to attend the symposium.

The videos are available via the following YouTube links:

Remy Allard
Stan Klein [Slides (with additional notes)]
Josh Solomon
Peter Neri
Keith May
Daniel Baker [Slides]

Details of the talks (including abstracts) are available here.

Many thanks to Udo Ernst and his team for hosting and filming the event, and Keith May for editing and uploading the videos.

Big ‘ooohs’ and big news

Last week I was in Sardinia for this year’s ECVP conference. Despite some bad weather, organisational problems, and the first venue I’ve been to without free wifi, it was a great week with some fantastic talks and posters. There was lots of nice food and company too, and we saw some amazing caves:
My talk was on the Tuesday, and was the first outing for a new size adaptation effect we discovered in the Aston lab. The room was stacked to the rafters, and I was very surprised at the response I got from the first demo video – everyone went “oooh” at the same time! There should be a write-up of the illusion coming soon in the Friday Illusion blog at New Scientist. [EDIT: Now live, here].
Also whilst in Sardinia, I had a job interview over Skype. A bit unconventional, but it seemed to work OK. Anyway, they must have liked me because they offered me the job! So, from this January I will be a lecturer in the Dept of Psychology at the University of York. I went for a visit this week, and it’s a lovely campus with a great department. Lots of interesting things going on to get involved with.