Tag: MATLAB

Making a poster in Inkscape

I went to Physiology 2016 at the end of July, and I presented what I think was definitively my Best Poster Ever.

 

Poster selfie!

A photo posted by Beth McMillan (@teraspawn) on

I usually make my posters in LibreOffice Impress, but this time I had some trouble with Impress crashing and so finally decided to make the switch to Inkscape, a free vector graphics program which works on Linux, Mac and Windows. I'd used it previously for making some vector graphics, but I still learned a lot of new tricks in making this.

One word of warning - I used the Linux version of Inkscape, and I'm not sure if everything's in the same menus for all versions.

Change page size

First things first: set the page size to your poster size. Mine was A0, which is an option in the list, but you can also enter custom values. Go to File > Document Properties > Page, or Ctrl-Shift-D > Page.

Navigating

I seem to constantly hide the scrollbars by accident. The shortcut to show/hide the scrollbars is Ctrl-B (you can see why I might have this issue...)

There are also some useful shortcuts for different zoom levels - 5 zooms out to show you the whole page and 1 gives you a 1:1 zoom.

Snap to Grid

First, show the grid by going to View > Grid, or #.

Then, tailor the grid to the size you want by going to File > Document Properties > Grids, or Ctrl-Shift-D > Grids. It's a good idea to change Spacing X and Spacing Y to integer divisions of the page size - e.g. I wanted 100 squares across on an A0 page, which is 841 mm, so I set the grid to 8.41 mm squares.

You want your boxes to line up, so select the "snap to grid" button from the top of the toolbar on the far right of the screen. To snap to grid when you're resizing boxes, select the "snap bounding boxes" button, which is the second button on the far right toolbar.

Align & Distribute

This toolbox was very useful for centring the titles of my boxes. Bring it up with Option > Align & Distribute, or Ctrl-Shift-A. Select a box and an element inside it, and then use the buttons to align the element with respect to the box.

Cropping images

To crop an image, create a rectangle the right size and position it over the original picture. Select both objects and go to Object > Clip > Set.

Group and Ungroup

When it comes time to reorganise sections on your poster, it's useful to select a whole area and group all of the objects together, so you can move them as one. If you want to edit an individual component of the group, you can then ungroup the items. Go to Object > Group or Object > Ungroup, or Ctrl-G/Ctrl-Shift-G.

Text boxes

Wrapping text in Inkscape has to be done in a somewhat roundabout way. First, make a box that is the size you want your paragraph to be. Then, select the text and the box and go to Text > Flow into Frame (or Alt-W).

It's a bad idea to resize a text box after you've created it, because you'll end up changing the font size while you do it. I'm not sure how to fix that problem! You can re-flow the text into the box if you need to change its shape.

Fonts

I like to use fonts other than the usual Calibri, Arial, or Times New Roman, just for a bit of variety. We're not talking Comic Sans or anything particularly wacky, but there's enough difference between even fairly conservative fonts to look a little different. Google Fonts is a useful resource for nice, downloadable fonts.

For the A0 poster I made for my latest conference, I was recommended to use a 96 point font for the title, 48 point for the section headings, and at least 26 point for axis labels. I used 32 point font for the body text, and I think it looked right.

Matlab figures

If you use Matlab for your figures, you can export them directly as vector images. I made a Matlab script for printing out an eps and a png of the active figure, given X and Y dimensions in cm and a filename: tidyprint.m

Logos and colours

I would hugely, massively, incredibly strongly recommend that you use vector versions of any logos or pictures that you include in your poster. Pixellation is incredibly noticeable, especially at the large sizes that you're likely to be using. For example, the EPSRC and Oxford both offer vector versions of their logos.

If you want to take some of your colour scheme colours from a logo or picture that you're using, the eyedropper tool (F7) lets you pick up and use a colour from anything in your document.

To make the built-in Inkscape palette a little easier to access, click the triangle to the right of it and select "wrap" so you can see them all at once.

It's important to make your poster colourblind-friendly. I was recommended the ColorBrewer website, which can create you a palette to use. In general, steer clear of rainbow palettes, and replace green-red pictures with magenta-cyan pictures.

I'm really happy with how my poster turned out in the end and I'm sticking with Inkscape for all future posters. I hope that these tips were useful - if you have any more, share them in the comments!

...

Hodgkin and Huxley's giant squid axon model

I deeply regret that I must begin this post by informing you that the entity in question is a giant axon from a squid, and not an axon from a giant squid. I can only imagine your disappointment on learning this fact - I recall that mine was considerable.

The models of heart cells that I'm working on at the moment are all based off a mathematical model from way back in 1952, created by Alan Hodgkin and Andrew Huxley. They described the electrical signal that passes down the axon of a squid's nerve cell when it is excited. The axon that controls the water jet propulsion system of a squid is particularly large, and easy to use in experiments.

The basis of this mathematical model is an understanding of the cellular features as components in an electrical circuit.* Just like in heart cells, the electrical signal is caused by the movement of charged particles, called ions, across the cell's outer membrane. The membrane of a neural cell acts like a capacitor, which means that ions accumulate on one side of the membrane, allowing it to store charge. This makes one side of the membrane more positive than the other side, leading to a voltage across the membrane.

This graph shows how the voltage across the membrane changes when the cell is stimulated.

An electrical impulse in an axon

The flow of ions across the membrane acts as an electrical current. Three types of ionic current are considered in this model: the sodium () ions that flow into the cell and cause depolarisation of the membrane, the potassium () ions that flow out to repolarise the membrane, and the "leak" current (a mixture of ions, including chloride ions), which flows in both directions.

Circuit description of nerve cell

The electrochemical gradients that power the flow of each type of ion are modelled as batteries, and the ion channels that permit ions to pass are represented by variable resistors.

is the stimulus current that the cell receives from outside.
and are the sodium, potassium and leak currents, respectively.
is the capacitance of the membrane (i.e. its ability to store charge)
is the membrane voltage
and are the resistance of the membrane to letting each type of ion through
and are the membrane potentials at which the flow of sodium, potassium or leak ions (respectively) through the membrane is zero.

Since the current across the capacitor depends on the change in voltage over time and on the capacitance (), and the four components of the current (that are wired in parallel) all add up to the stimulus current (), a unifying differential equation can be created.

Where , i.e. the difference between the current membrane voltage and the usual, or "resting" voltage.

The next part of the paper deals with the gating mechanisms for the ion flows. My plan is to tackle that next week!

The original paper is available free from PubMed Central here. There's also a very good description of its content on Wikipedia, and an illustrated XML version of the model at the CellML model repository.

I put together some MATLAB code to solve the equations described in the paper - you can download and view or run the source code here.

One of the most interesting features of this paper are its descriptions of a possible mechanistic basis for the permeability of the cell membrane to ions. This paper was written long before ion channels were discovered and characterised in mammalian cells, so it's amazing how accurately it describes the action of the nerve cell. (A very readable account of the history of ion channels is available on Montana State University's webpage here, incidentally).

* which I'm sure is a helpful explanatory device for people who have the foggiest concept of how electricity works. I am not one of these people. I've relied on some A-level revision websites and my various physicist chums/siblings for that.

...