Category: Software for manuscripts and figures

• Extracting data from published graphs in Matlab

  Have you ever needed to grab data from a published graph, perhaps to reanalyze the results? The grabit function, available on Matlab Central, does exactly this. It’s a GUI that allows the user to specify the location of axes, and then grab data by clicking on the data points. Learned about it in the Methods…

  March 1, 2012

• Smoothing a non-uniformly sampled surface

  Working with 2d data defined on a grid is pretty straightforward in Matlab; you can easily visualize the data with imagesc and smooth it through convolution. Working with data sampled at non-uniform intervals is much trickier. Doing something as simple as visualizing it becomes a pain. One way of getting around this is to resample…

  February 4, 2012

• Converting Word 2007 equations into 2003 or MathType equations

  I used the Word 2007 equation editor for a recent paper. I like the editor because it supports TeX-like commands. Unfortunately some journals do not support Word 2007 equations. PLoS Biology suggest saving down as Word 2003 and recreating the equations manually. Argh, that sounds like a terrible way to spend an afternoon. Thankfully, MathType…

  June 8, 2011

• Citation management with Zotero

  I’ve grown increasingly frustrated with EndNote, its awkward interface and buggy Word integration. I’ve looked at a few alternate solutions: Mendeley, Papers, CiteULike. I ended up settling for Zotero, which I now love. I don’t think it makes any sense for a citation management software to use ask you to use its own internal search…

  May 16, 2011

• Video tutorial: Adobe Illustrator for scientists

  Adobe Illustrator is an ancient program with obscure features that can be extremely frustrating to use if you don’t know its ins and outs. Once you do know how to use it well, however, it is incredibly powerful. I’ve create this Adobe Illustrator for scientists tutorial on YouTube. The tutorial lasts 1h45 minutesI have optimized…

  June 19, 2010

• Batch export .ai files to pdf

  March 2020 update: several blog readers have said that this works up to Illustrator CC 2018. Let me  know if you have success on newer Illustrator versions. Every time I send a copy of the current version of a manuscript to contributors, I have to export .ai files to .pdf (they can’t read .ai) for…

  May 12, 2010