Down on the (Visio)-pharm

Since my first post on the blog four years and a month ago, I’m moving on from a my role at the Liverpool Centre for Cell Imaging to pastures new. As of April 2019, I’ll be working as a Technical Specialist with Visiopharm, helping to develop their business in the UK and Latin Europe.

As this blog was chiefly in use as a repository of information and curiosities from projects and users that I encountered during my work at the CCI, it’s unlikely there will be many posts in the near future. Who knows maybe the blog will live on in the hands of the next Image Analyst.


Pivot (-table) on a dime

Much of the posts on this blog deal with converting Images to numbers, which is what I would consider Image Analysis. This is ususally followed by some method of data analysis (converting numbers into results or other meaningful output.

This post will deal with the latter, and chiefly using Pivot tables to easily summarise the sorts of data that will frequently come out of Imaging experiments.

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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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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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