ImageJ

ImageJ and Volume Measurement

In which I describe the complexities of analysing 3D images...

3D image analysis just seems to be one of those things that is harder to do than I'd like it to be.

Before starting it is worth pointing out that with MRI you can acquire volumes in two ways - traditional 2D with multiple slices or a 3D scan. As far as this blog post is concerned these are the same.*

A common measure in clinical MRI is the volume of an organ or part of an organ. After all when someone has brain cancer - "How big is the tumour?" can be a very important question. Here are my experiences of trying to measure volumes on MRI images.

*There are differences between these two methods of acquisition but that would require a whole blog post on it's own.

CASE Placements and Research Software

In which I apologise for this week being low on blog posts and update you on my AstraZeneca placement. Also I use software I normally use for research for other purposes.I'm sorry there haven't been any updates this week. There was no cake made as I had no time for choir on Tuesday, no tea as it's an alternate week and the usual Thor update is delayed (pending a hot wire cutter).

CASE Placement

This week I started my work placement at AstraZeneca, the industrial part of my Industrial CASE PhD (see my post on PhD types). Apart from the system shock due to waking up significantly earlier than usual (my commute to UoM is a 15-20 min walk not a 45-60 min drive) the week has been good so far :) I've gone through a load of induction sessions and lots of positive feedback on my study designs and planning for the weeks ahead.

Next week I start work proper with my first study and hopefully the results will be as we predict. Sadly for now I can't give any more details due to confidentiality agreements. Rest assured though if I get a publication out of this placement (which I hope I will) it will be mentioned in this blog :)

Weeping Womble

On Monday night I managed to take a good set of photos of fellow Scout leader and Networker (Womble) walking ominously towards my camera. I used ImageJ a free, java based image tool commonly used by MRI researchers to animate this simple gif:

Weeping Womble (640)

After fixing some timing issues, adding 'blinks' and a final word of warning I ended up with this final masterpiece of internet animation:

Weeping Womble Final (640)

Proof that research software can be quite fun in your spare time!

Tom Out!

P.S. AstraZeneca

P.P.S ImageJ