Category Archives: Aside

How Revealing!

As part of the 2018 CCI Imaging Workshop, I ran a guided hands-on about using Fiji for Image Analysis. The workshop was aimed at complete novice and intermediate level users. The slides and materials were delivered through a web browser using the Reval.js framework, and this post will be a few more details on that framework and how (and why) I think it’s really useful for this sort of thing. Let’s get revealing!

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More Notes to the Future

Instead of talking about image analysis, this post will document the setup of a multiuser multisite ELN based on WordPress. Lots of the hard work was done by Steve Royle and detailed on his blog here and here. I found his technical post immeasurably helpful so to pay it forward, I wanted to share the details of our setup.

Apologies to anyone not dealing with the sysadmin side of things. You may want to skip this one.

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Making it up (Part 1)

Whenever you’re testing a new analysis protocol or playing around with some software, it’s always handy to have some sample data to mess with. But what if you don’t yet have the data, or what if you need more, or need more specific data? In this post, we’re going to delve into the world of synthetic data by making a sample tracking data set.

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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...");

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