Tag Archives: Scripting

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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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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Navigating Multidimensional Datasets with Simple Macros

Replication is key to the Scientific method. This is especially true when dealing with imaging, when a single field (at any magnification) is rarely representative of the entire experiment, let alone the underlying phenomenon as a whole. The easy solution to this is to take many fields of many samples, but visualising and manipulating a whole dataset can be a time consuming endeavour. In this post, we’re going to cover some of the tricks for working with a dataset in Fiji and take the first steps into the big wide world of scripting.

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