Friday, 18 July 2014

Microscope webcam microtitre plate reading using image analysis

An A-level student has just spent two weeks with us for his work experience, and his project has been to investigate the use of a cheap microscope webcam as an alternative to an expensive plate reader for the measurement of the growth of yeast in microtitre plates. The longer term aim would be to mount this webcam on the deck of our Tecan Genesis liquid handler robot, and to have the robot arm move the plate under the webcam.

The webcam is a Veho VMS-004, used at 20x magnification, and it costs just £40. It was recognised automatically by Linux as a webcam and worked really well with the OpenCV library.
Robert Buchan-Terrey did an excellent job in interdisciplinary science in just two weeks, including the following:
  • Preparing media and growing yeast in our lab
  • Pipetting the yeast to make dilutions
  • Using the microscope webcam, taking images of the wells in the plate at intervals throughout the day, and corresponding plate readings with a real plate reader
  • Coding using Python and OpenCV to process the images (find the circular well, work out the average pixel intensity in the well)
  • Data analysis and stats to understand the results
He also produced a poster to demonstrate the findings and to take back to his school.

And the answer is: although he's just analysed the data from one time point so far, and we took no care to make sure the lighting conditions were stable when taking the images, or to shake the plates to evenly disperse the yeast, it really does look very plausible that we could use this in future. Averaging over 8 replicate wells gives a remarkable correspondence between image-analysis results and plate reader results. Individual wells are more variable, but still show promise. We've yet to test all the data, and to test the full range of the scale of optical density, but this looks extremely exciting.

Thanks very much to Wayne Aubrey and Hannah Dee for their help and expertise with the yeast biology and the image processing respectively.

Saturday, 21 June 2014

The Genome Game with Countdown and High Score Table

The Genome Game now has a part where you have to guess the rules (correspondence between genotype and phenotype) before the time runs out. If you guess correctly then you get to join the (local storage) high score table. It's also bilingual now, so you can play in the medium of Welsh.

Friday, 13 June 2014

Sewable wearable computing

I gave this as a very short talk at the recent BCS Mid-Wales Show and Tell. So I'm describing it here in case it's of use to others.  The presentation was mostly a collection of rather large photos but it can be downloaded at I was inspired to give it a go by Charlotte Godley (@charwarz on Twitter) who ran a wearables workshop for Girl Guides using Adafruit Gemmas.  These are small Arduino chips on a mounted on a base, made by a company called Adafruit. The base has holes so that you can sew it onto items of clothing. Slide 2 shows a Gemma attached by crocodile clips to an LED, a light that can be programmed to flash in any colour. The Gemmas are very cheap, only £6.50 so you can safely play with electronics without spending too much if you break it.

Steel thread can be used to sew your Gemma to its LEDs. This conducts and so replaces the crocodile clips (or soldering bits of metal) when you want to make wearable electronics. It's not that easy to sew. It doesn't bend and tie as easily as thread does, and can come undone, and make short circuits when it crosses other bits of thread. Also, the longer the thread, the higher the resistance.

After the Gemma, I got a Flora, it's bigger sister. This costs approx £20, and has more available connections. I wanted to attach an accelerometer and lights, and have the lights flash different colours in order to demonstrate the x, y or z direction of movement. The presentation shows how I put it together and how much it cost. You can see how it was stitched, how I used nail varnish to stop the knots in the ends of the steel thread from unravelling, and how it gets programmed using the Arduino environment.

The Adafruit site has a lot of useful explanations and videos about the Gemma and the Flora. You can buy the equipment from many sites (I used Phenoptix and 4tronix, both were good).

Overall, it was fiddly, but a lot of fun. Computing projects that have an element of real hardware, poor connections, and many parts, each of which could be wrong, are always harder to debug than software. I've never really played with electronics before, and I ended up learning a lot even in this simple project, about power, resistance and circuits. And I now have a thing with flashing lights that I can wear on my leg while dancing the Charleston.

Sunday, 20 April 2014

Lovelace Colloquium 2014

This year I'm not going to write about the fact that the Lovelace Colloquium is for women undergraduates in computer science because I already did this in 2012 and 2013. And I won't write about how much fun it was this year, because Charlotte has already done that.

I'm just going to mention that after the conference, on the way home, changing trains at Birmingham International, I went to browse WHSmiths for something to read on the train.

Yes, the computing magazines are in the section labelled "Mens Lifestyle". Not for us women. We can have interiors, weddings, home and travel. I don't know why even WHSmiths wants to discourage us from computing. Why do they need to separate the magazines by gender instead of by topic anyway?

Then, on the train, I saw a blog post on my twitter feed about the NSF Waterman award, which has been won by men for the last 10 years in a row.  All I can hope is that the women undergrads who entered and presented at Lovelace 2014 will now continue to enter many competitions for their work in science, to continue to present their work at conferences, to feel that they can enjoy computer science (whatever our high street shops try to tell us) and to win far more recognition than we do at present.

Update: Also see what Michelle Brown thought of Lovelace 2014.

Monday, 3 March 2014

Western Mail article about bioinformatics

As part of the Welsh Crucible I had an article in the Western Mail today. How computer science can solve problems in biology. We were asked to explain our work in 400-500 words (they chose the title). Much more challenging than I thought it would be, because that's not very many words.

Thursday, 6 February 2014

Final year computer science projects

This term I'm supervising 5 final year student projects. They have one term (just over 3 months) in which to really create something they can be proud of. It's not long, especially when they have to get to grips with new terminology, new equipment, reading and research, specification, design, implementation and experiments, testing, documentation and reflection. They're also asked to keep progress diaries or blogs and use version control to manage their projects.

I've very excited about the projects this year, they're all diverse and fun:

  • Using information theory and machine learning to recognise quality control issues in next gen sequencing lanelets (together with Joshua Randall, Sanger Institute)
  • Analysis of the content of NLW's digitised newspapers collection
  • Modelling insect choice among plants (together with Lizzy Donkin and John Warren in IBERS)
  • A model of the brain of C. elegans that we can play with as a talking point in AI discussions with the public.
  • Using image processing and microscope webcams to determine the growth of yeast in microtitre plates.

Hopefully, we'll have some good results by May!

Bioinformatics and computational biology: 500 years of exciting problems?

I gave a talk at Warwick University, Department of Computer Science in January 2014. A look at the intertwining of computer science and biology from the days of Turing through the present and on to the future, including some of my research along the way. 
In a 1993 interview, Donald Knuth worried that computer science in the future will be "pretty much working on refinements of well-explored things", whereas "Biology easily has 500 years of exciting problems to work on". I'll describe some of the bioinformatics and computational biology that I've been working on. My talk included a little about where the field has come from, where it's going in the future, and whether it should be considered a branch of computer science at all.
The slides are online at Figshare.

Sunday, 5 January 2014

Storm damage in Aberystwyth in January 2014 and in January 1890

An unusually high tide in Aberystwyth in January 2014 has severely damaged the promenade. We do get some spectacular weather here on the west coast of Wales.

Broken railings and paving on Aberystwyth promenade.

Forceful storms that broke up the promenade also occurred in other years, particularly in 1927 and 1938, and their aftermath was photographed and looks remarkably similar. In January 1890, the Cambrian News reported a storm at Aberystwyth which caused trouble to the train travelling between Aberystwyth and Machynlleth.

"The uptrain from Aberystwyth had to wait in the Junction for over half an hour until the tide had partially subsided. Then the line was cleared of pieces of timber and accumulations of grass and rushes and the train proceeded, though the water was half way up the wheels."

Would the Junction that was referred to here be Dyfi Junction station? The storm in 1890 also caused a hole in the sea wall, in a very similar location to the one that's been opened up this year:

"Unfortunately, the masonry forming the slipway near the Queen's Hotel gave way and subsequently a large hole was washed in the sea wall"

The Queen's Hotel is no longer a hotel, but still exists as a building. It has been used for many purposes since 1890, and has most recently been used as council offices and archives. It's currently up for sale, at a price of approximately £1 million.

The hole in the sea wall caused by this year's weather shows just how powerful the sea is against our buildings and defences.

And in 1890 a steamer in distress was spotted out in the bay, carrying a cargo of pig-iron but having lost its funnel in the storm. The lifeboat was launched, under the command of a Mr Tom Williams, and the crew were rescued and taken to the Belle Vue Hotel for "much-needed refreshments". Our lifeboat was also out rescuing in 2014 and, so far, everyone's safe and sound.

Waves wash over the promenade in front of Alexandra Hall and flood the ground floor.

More photos of what happened in 2014 are on Flickr.