Tools for Open Access Research

As it’s Open Access week, I’ve decided to write a post about Open Access in the context of software, file formats and Imaging Data.

So what’s the problem?

We’ve all been there. Picking up a project from someone else, downloading data from a repository or using an ancient piece of equipment leaves you with an obscure file format you’ve never heard of. What am I supposed to do with a .dnm file? Worse, you might have a proprietary file format whose association you know but that can only be opened by a piece of software that doesn’t run on (Windows|GNU/Linux|Mac) or perhaps is prohibitively expensive.

Part of Open Access is all about making these sorts of problems a thing of the past and making data accessible to anyone who may want them. There are already some great pieces of free software available (which are free like beer and speech). Importantly, these are often open source, which usually allows others to adapt or remix the software, increasing the support and lifetime of the program.

Below are some of the software that I regularly come across in my work as Image Analyst at the Liverpool Centre for Cell Imaging, split up into categories to keep things tidy.

Images by the numbers

Unless you build your own microscopes (and there’s an open source solution for that too!), you’ll be buying your microscope from one of the big manufacturers. The problem is that each one has it’s own standards and proprietary file formats. Traditionally, if you used a Nikon, you would need to install Elements; if you use an Olympus, you’d need to install Fluorview, and so on. If you use multiple manufacturers, you’d have to install lots of different software with varying analytical ability (and the aforementioned platform restrictions), just to process the images before even embarking on data analysis.

2016-10-oaweek_mason_001

Thankfully (and unsurprisingly if you’ve read this blog before) this problem is easily solved with Fiji which comes bundled with Bio-Formats, which not only allows opening of basically every proprietary format (including some AFM ‘images’) but also parses a good deal of the valuable metadata from the files.

I could go on all day about Fiji, but as PostAcquisition is basically homage to it and all it can do, I’ll leave it there.

Go Figure

Research is partly about finding things out but also about communicating those things, to peers, the scientific community and to the general public (who, after all, fund much of the work we do). When work is published, scientists create Figures to support the text of a manuscript. I think it’s fair to say that most people currently use closed-source software like Corel Draw, Adobe Illustrator or Microsoft Powerpoint to make figures.

2016-01-GoFigure_109

So what if you’re trying to share files with collaborators who don’t share your site licence? What if you want to upload your figures to an online repository so people of the world can download and use your beautiful vector graphics? Enter Inkscape. If you have experience with Adobe Illustrator the learning curve is basically non-existent, you’ll find all of the tools and functionality you know and love in a vector graphics program plus, you can install as many copies as you want at home and/or work.

2016-01-GoFigure_003

You can find a couple of posts about how to make figures in Inkscape, but it doesn’t stop there; you can use it for conference posters, signs, handouts and teaching materials to name but a few.

Fancy re-writing part of the program or extending functionality with a plugin? Check out the source code and get cracking.

Productivity

Like Hoover and Kleenex, Microsoft Office has become synonymous with spreadsheet and word processor. Many people use them because they have always used them and are not aware that there is an alternative. There is! and if you’re looking for a replacement, LibreOffice is a great choice. Once again, if you’ve used a spreadsheet or word processor before, you’ll basically have nothing new to learn.

All of the file formats you already have (xls, ppt, docx) are supported including the ability to natively write PDFs (which in fairness you can also now do in Office).

Build your own world

Computer Aided Design (CAD) has been around for a long time, to help with the design and production of prototype or manufactured parts. With 3D printers becoming more and more affordable, there’s no surprise that there are plenty of people designing and building parts. There are plenty of (closed and open source) 3D modelling programs out there, probably the most notable are Blender and (my current favourite) FreeCAD. Both of these can output STL files for 3D printing.

montage

Not just hating on Commercial Software

It’s very hard to write a post like this without making it sound like I think we should all get everything for free and switch to free (like beer) software, which is not my perspective at all.

Firstly, if you use these software, I would highly recommend supporting them. This can be financially (the difference being, you get to decide how much you want to ‘pay’ for them) or by promoting your experience with them. Why not tweet, blog or write about the software. Even better, become an active member of the community: report bugs, write tutorials, you could even start blogging.

Secondly, I fully accept that there are plenty of reasons why you might want to use (and thus pay to support the development of) commercial software. We use Bitplane Imaris for a lot of our 4D visualisation and analysis. Also, I have over a decade of experience writing Visual Basic for Applications code, so I’m not quite ready to switch to LibreOffice Basic, even though the support for VBA is getting better.

The last word

Whatever piece of software you choose, try to think about making your files as accessible as possible. This can be done largely by avoiding obscure and likely short-lived formats in favour of something openly documented.

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