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!
The style of this post is going to be a bit different than the usual PA posts, but I though this journey was worth documenting somewhere on the off chance it’s helpful.
So here we go: how to pick random ROIs within an original area.
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.
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.
In this post, we’re going to look at how to use Fiji to add annotations to an image. Arrows, asterisks and text are all added in roughly the same way. Here’s how:
In the last post, I covered the basics of wound-healing assays and how to quantify and visualise them. This is great, but is the ability of cells to heal an artificial wound really what you want to measure? Probably not…
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..."); //run("Macro");
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