uon-2021-summer-brains

Some neuroscience notes

denis schluppeck

2021-05-24

this repo contains some tips, tricks and a couple of projects related to finding out what neuroscience at university is like. It was prompted by discussions with a couple of budding scientists (a couple still at high school), who wanted to find out a bit more about doing research.

plan

• some julia notebooks and youtube clips to go along with them, explaining

  • how to look at images (in general, and brain images more specifically)
  • make visual stimuli (inspired by ideas from face-spaces, etc)
  • think aboug showing images, visualising data, plotting graphs
  • start thinking about designing experiments to ask (and answer questions)
  • whatever comes up during discussions

julia note book stuff

I will try to post some notes and details to help with julia stuff here as we go through things and if we manage to find time for some follow-up sessions.

To get started with the julia notebook in this folder:

• start julia
• at the prompt, type ] the open square bracket
• and activate the evironment by typing activate .
• make sure you have the packages installed with instantiate
• the start the Pluto notebook with Pluto.run() and opening the brain-notebook.jl

I have made a little youtube clip walking through the steps…:

1. first steps with the julia notebooks: https://www.youtube.com/watch?v=OTVC4D3SC6U
2. try to find out a bit about julia environments - this will help you with some of the package dependencies
3. There is a brilliant online course (at MIT), where you can get some tips - https://computationalthinking.mit.edu/Spring21/
4. maybe especially useful about how to set up the software etc. - https://computationalthinking.mit.edu/Spring21/installation/

things I mentioned in the youtube clips / on slack

• a possible solution for working with audio. In this case actually recording a snippet and saving it out – but you could adapt to make your own wave-forms and play around see audio-demo.jl

• some snippets of code for working with the allFaces.mat data (stack of images). Pointers on how to calculate the mean across all faces, display them, etc. see average-faces.jl

text editor + other things

• it’s a really good idea to have a good / powerful text editor (not word, because that can mess things up :). I now use Visual Studio Code (free) from Microscort – which is very good: https://code.visualstudio.com/

specific ideas / problem sets

1. Images are tables / grids of numbers
2. In julia, write a function that takes a list of numbers like [1.2, 4.5, 3.6, 1.4] and turns it into a table. In the case of n^2 elements into a table with n rows and n columns
   • is there more than one way to make this table?
   • what would you have to know if the table / image was not square?
   • can you think of a way to make this function more generic, so it can handle rectangular tables / images, too? What’s needed for this?
3. Can you think of a way to do the reverse (table -> list or vector)? What are some of the issues here?
4. Using the julia packages Images, MAT, and NIfTI, can you figure out a way to load in a PNG image, a MAT file and a NIFTI file respectively?
   • Can you find out what each of those formats is routinely used for?

make use of the slack

https://uon2021summer-2sl7364.slack.com/

It might be a really good idea to talk to each other on the slack channel to discuss ideas, where you are getting stuck, what some of the possible solutions might be… it’s much easier to learn this stuff in a group

While I am away from e-mail, I will ask if a couple of my PhD students are able to pop onto the slack every now and then to help with generic answers…. (they are most likely to be matlab and python users, so may not be able to help with julia questions, though 😀)