Other Utilities and Helpful Routines

As well as Figure Maker, there are a number of other useful routines availble.

Figure Utilities

Check whether your figure or image is colour blind safe using this simple utility Check_Colour_blindess.ijm.

Blind Analysis

BlindAnalysis.ijm Takes a directory of TIFFs, strips the label from them and saves them with a blinded name. A tsv called log.txt is created to log the association between the original file and the blinded copy. Works on TIFF only.

ELN Saver

This is a simple utility to save a version of the file you are viewing in Fiji/ImageJ to put in your electronic lab notebook. A png version or low-res movie of the file you are looking at is saved to the Desktop with a unique name. A text file is saved to explain the filenames.

Movie Annotation

Two macros that will:

1. Add arrows to movies to highlight and track an object of interest. Unlike other scripts out there, this one places an arrowhead in a fixed orientation/distance from the object and allows annotations in any frame (not all frames).
2. Irregular Time Stamps - adds timestamps to movies, formatting them in hh:mm or mm:ss. Unlike other versions, negative times are allowed and the time intervals do not have to be regular. Requires a new line separated text file of times.

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Other utilities

In qUtils there are some other utility macros that we use in the lab.

We've had problems with nd2 files being saved with a LUT that is not pure red, pure green or pure blue. This is because it uses a LUT that is based on absolute wavelengths of the fluorophore. You can use Make_NIS_Pure_RGB.ijm to sort out the colours.

Open all the nd2 files in a directory and save them as TIFF to another directory with nd2SaveAsTiff.ijm.

Maybe you like to open a whole directory of images, look through them, closing the bad ones and leaving the good ones open. Perhaps you want to grab the list of good images so that you can come back to it later? Well, PrintTitlesOfNiceImages.ijm does this for you.