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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Random Access MemoROI

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.

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Correcting the record

Unless your imaging facility is in a clean room (and you never touch it), from time to time, we all end up with unsightly splotches on our transmitted light images. The best fix for this is to clean the microscope but sometimes you just have to do what you can with what you’ve got.

Thankfully there’s a fairly easy way to correct it post-acquisition. Let’s Flat-field correct!

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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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Staying in (version) control

As part of my job, I find myself writing lots of bits of code for people. Until quite recently, my version control system was renaming the files and commenting in the header to keep track of changes.

Not the tidiest system

I say “quite recently” as I started using git as my version control system and have not looked back. I’m by no means an expert, but in this post, I’m going to give an introduction to using git in the context of scripting.

This post is really aimed at people who have no experience with version control systems or have heard about git but have never really used it (or have tried and failed to get the hang of it as I did…twice).

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In the Bin

A lot of work we do at the CCI uses scanning confocal microscopes, which have the advantage that the operator can pick the number of pixels in X and Y that will make up the final image.

For camera-based systems this is a less simple endeavour as the array of the CCD chip is fixed. For this reason, we may want to downsample or bin our images. In this post we’ll cover a bit of theory and details on how (and why) to bin your images.

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Thoughts on #LiveTweeting

Blog and Log

As a part of the Centre for Cell Imaging and a member of the Microscopy and BioImage Analysis community, I occasionally get away to conferences like the recent NEUBIAS training school and symposium in Portugal.

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Since having joined Twitter last year (@dn_mason), this is the second conference that I’ve been to, and as a result, was the second time I tried (with reasonable success) to Live Tweet at the conference.

Live What Now?

Going right back to basics, Twitter is a platform for broadcasting small messages (of ~140 characters). Some describe it as micro-blogging. To many, the brevity of each tweet is both it’s greatest strength and also one of the most frustrating features.

Live tweeting, is basically the act of providing a running commentary of a seminar, event or even a whole conference. All of the tweets associated with such an event can be tied together using…

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