I wrote and successfully ran my first Macro….I have no idea what Macro means but I know it’s a piece of code used to perform a function on my computer.
I have entered the phase of data analysis in my PhD. If feels like my entire life is trapped within this little black box supposedly filled with 2 terabytes of digital what-not. As a potential future doctor of philosophy I have been stretching and yoga-ing my brain muscles and attempting to use higher order thought processing (in other words, how can I get more done in less time).
One of the numerous digital hurdles I’m entering into, is dealing with blood smears. On the tundra during summer in Nunavut our team captures breeding shorebirds and takes a variety of quick samples including a drop of blood. This drop (or even smaller than a drop) is smeared on a glass slide to generate a single layer of red blood cells so we can see them under a microscope.
Each slide contains hundreds of thousands (or even gazillions) of cells. Often scientists report the number of different cells or the prevalence of infection/disease within an observed 10,000 cells. It’s easy to miss the odd infected cell so the greater the number of cells the better. That’s all fine and dandy but counting 10,000 cells per blood slide for over 150 birds is just not what I want to be doing for 6 months of my life straight. My time is much better spent using my brain to do ‘science’ interspersed with watching Netflix or knitting baby hats.
So I took to the world of code and programming to solve this seemingly impossible endeavor.
Little did I know…..stuff like this can be really easy. There is definitely some trial and error but free software (Imagej) and a macro (some code thing) can run a batch containing all my images and count the cells for me.
Download Imagej if you are ever counting cells. And process your image using a macro like mine:
Convert the colours in the image to something recognizable for the program and then tell the program to count the number of those things…..
Hit the process button under a Batch function to run the macro for a whole suit of images and watch the magic happen (or don’t watch; just walk away and let your computer work). I was able to count 10,000 cells in just over 200 images in 10 minutes. I would have walked away and done something fun like eat cookies but I was sitting on a plane on my way to Seattle. Plus, I was so stoked ‘something was happening’ that I sat starring at the screen praying my computer didn’t suddenly self-destruct.
So next time you are faced with the challenge of managing large amounts of data, or with technology in general, try to experiment with some different options out there to save you time. Most of the papers out there say “we counted 10,000 cells per slide for the 1000 individuals of mice to determine….something something”, and what it should say is, “A poor unsuspecting undergrad student was roped into volunteering to count slides for 12 hours per week for 2 whole years to determine…..something something”. Likely most of us don’t have the luxury of hiring technicians or bribing undergrads with Tim Horton’s gift certificates to work endlessly on something mind numbing. So scientists, “don’t always just work harder, work smarter”, so you can free up time to have fun, (like get on a plane to somewhere exotic) life is too short to count red blood cells.