Monthly Archives: June 2015

Having Contractions!

One of the major advantages of having environmental control on our microscopes at the CCI, is that you can get cells to behave a little more like they do in an animal or plant. A great example of this is when looking at cardiomyocytes that can spontaneously start to contract when grown in culture. You can see a load of these on YouTube.

These types of culture are a great model with which to study the effect of drugs or other treatments on the cells of the heart. This post will look at one way to quantify contractile motion without the need for exogenous stains or dyes (which can themselves perturb physiological behaviour).

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It’s a Stitch up!

Scale is a funny thing. To virologists, bacteria are big. To microbiologists, cells are big. To cell biologists, tissues are big. We’ll not go as far as the cosmologists, but the point is that sometimes you have to move out of your size-based comfort zone and image something BIG. Enter imaging tiling!


Once you’ve acquired all of your images (36 in the example above), it’s not always clear (even in vendor software) how to put them back together. Today’s post will deal with image stitching and also cover one of the big problems you may run into along the way.

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ASIDE: Fiji Startup Macros

A quick pro-tip to follow up on the last post.

I use the Bio-Formats plugins all the time, so I like to have the shortcut window open automatically whenever I open Fiji. To do this, make a text file containing the line:

run("Bio-Formats Plugins Shortcut Window");

Save this file (it can have any name as long as the extension is .ijm) to:


This macro will now get run every time Fiji starts and the Bio-Formats shortcut window will appear. You can add anything you like to the startup macro. Mine includes a few other things and looks like this:

run("Options...", "iterations=1 black count=1"); // set black background
run("Colors...", "foreground=white background=black selection=yellow"); // set colors
run("Appearance...", " "); // do not use Inverting LUT
run("Bio-Formats Plugins Shortcut Window");
run("Channels Tool...");

//run("ROI Manager...");
//run("Control Panel...");

Double forward slashes are comments and are ignored.

Time to Downsize

One of the biggest challenges in modern Imaging Research lies in how to handle big datasets. This is a particular issue when undertaking multidimensional acquisition. In this post, I’ll be covering some ideas on how to sensibly work with large datasets as well as some neat tricks on how to downsize the biggest ones.


Multidimensional datasets can have multiple timepoints, channels, slices, positions or combinations of all of these.

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