The Process_Folder template in Fiji is a wonderful thing. It’s the starting point of most of the ImageJ macros that we use in the lab. However, it has a problem. This post is about how to fix it. tl;dr use this gist instead of the built-in template. The Process_Folder template If you’re reading this, you […]
Tag: tftb
Smaller: methods to reduce the size of a PDF file
Hot on the heals of the post on how to downsize microscopy movie files, let’s look at ways to shrink the size of a PDF file. There’s several ways to tackle this – suggestions came from this thread on Mastodon. Scenario: you have created a preprint/manuscript/proposal in PDF format. It looks great and is 18.4 […]
Tips from the Blog XVI: getting FASTA sequences
I am having some fun running AlphaPulldown on a computing cluster. A requirement is to have input sequences in FASTA format. I found that I needed to get ~600 sequences. I had a list of the relevant Uniprot IDs. Surely getting the sequences for these proteins should be straightforward? Solution The Uniprot IDs can be […]
Tips From The Blog XIX: initialising a new RStudio project
I like to set up a standardised directory structure for RStudio projects. The idea came from here. In brief, the structure is: My typical workflow is therefore to: So far, so good. However, this process is a bit tedious. I find it irritating to open up RStudio (which opens up a previous project by default) […]
Over and Over: quick ways to reuse handy shell one-liners
There are a few one-liners that I use in the shell to do some really nifty stuff. I struggle to quickly find and reuse these and asked for a solution on Mastodon. A handy one-liner might be something like (taken from here): This converts all the flac files in subfolders into mp3 files. Obviously, we […]
Tips From The Blog XVIII: upgrading a Music/iTunes library
Niche tech tips are the cornerstone of this website, and here is another. How to upgrade an iTunes/Music library whilst maintaining the database. I know everyone streams music these days – hence this is likely a very niche tech tip – but I still maintain a large music database on a server. The data in […]
Tips From The Blog XVII: determining playback speed of a video
Generating movie files for publication can be a bit tricky. We have a protocol for making them for microscopy data, which simplifies things. However, we recently got this question from a journal: please state the playback speed of each movie file How can we do this? What information is needed for movie files? Usually movies […]
Tips From The Blog XVI: fast check of two directories
Here is a quick method for checking parity between two directories. Let’s say we have two directories dir1 and dir2. They are large and have thousands of files and subdirectories. How can we check that they have the same contents? I found myself in this situation recently during a server migration. Method 1: rsync To […]
Convertible: using ffmpeg to convert audio files
A quick tech tip. I usually use Audacity for converting audio files and I have a few simple macros set up in there to make life easy. I had some opus music files which do not play in Apple’s Music app and therefore needed converting to MP3 format. Annoyingly, Audacity 3.1.2 on macOS does not […]
Tips from the Blog XV: locating the php.ini file for WordPress on Raspberry Pi
If I struggle to find the answer to something, it must be worth a post to help out others. So, here’s where to find the php.ini file on a standard WordPress install on Raspberry Pi. I installed a LAMP stack and WordPress on a Raspberry Pi following these excellent instructions. The aim was to import […]
