3. Macro recording

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Learning Objectives

Recording with the Recorder tool
Building macros using the Recorder output
Beginning to code in ImageJ

The Recorder Tool

Most processes in ImageJ can be recorded, enabling the fast and simple construction of code to automate analysis or image processing pipelines.

Let's try automating some of the processes we've already covered as an example.

Exercise 1: Using the Recorder

Open the Recorder

Plugins > Macros > Record

Open the Mitosis image we used previously in our figure ("Mitosis (5D stack)")
See that some text has appeared in the recorder. This is code documenting your actions. This is code documenting your actions.
By defauly the ImageJ Macro lannguage (simply called "Macro" here) is used. But the recorder will also produce records in other languages

Have a look in the "Record:" drop down menu

You can create a script directly from the Recorder by clicking "Create". This will be given the title present in the "Name:" text box

You can also open new scripts by File > New > Script

Note: It is possible to write code in ImageJ using even more languages. For your code to work, make sure the correct language is selected in the "Language" tab. For our current purposes we'll stick with ImageJ Macro

Scripts can be run by clicking "Run" or pressing Ctrl+R

Close the Mitosis image and try running the code you've recorded
This should reopen your image

Note: Individual images can be closed using the Ctrl+W shortcut, and Ctrl+Shift+W can be used to close all open image windows

Exercise 2: Building a script with the Recorder

Here we're going to try automate the construction of our figure from Page 2.

The only two parts of the process which required manual involvement were the adjustment of the image brightness and the selection of an ROI to crop the image.

It is possible to build manual intervention steps into a macro, but for simplicity we'll skip that step for now.

These were the steps. You can type the underlined commands into the search bar to find them again. Try to build a script to replicate this process:

Open Mitosis (5D stack)
Z Project...
Duplicate frames 25-28
Convert image type to RGB Color
Stack to Images
Select the first frame from the separated stack

Select the window with the cursor, or by Window > MAX_mitosis-1-0001

Add Scale bar
Flatten the scale bar onto the image

Your code should look something like this:

run("Mitosis (5D stack)");

run("Z Project...", "projection=[Max Intensity] all");

run("Duplicate...", "duplicate frames=25-28");

run("RGB Color", "frames");

run("Stack to Images");

selectWindow("MAX_mitosis-1-0001");

run("Scale Bar...", "width=5 height=7 thickness=2 font=14 color=White background=None location=[Lower Right] horizontal bold hide overlay");

run("Flatten");

Being a human, it can be difficult to keep track of what all the steps of a program are for. Particularly if they have been written by someone else!

It's good practice to write comments throughout the code, by preceedng text with // to annotate it.

You'll thank yourself later. E.g.

//This script will open the stock image "mitosis (5D stack)" and process it to make images for a figure

run("Mitosis (5D stack)"); //Open mitosis image

run("Z Project...", "projection=[Max Intensity] all"); //Maximum intensity projection to remove z-dimension

run("Duplicate...", "duplicate frames=25-28"); //Duplicate only frames 25-28 of the image

run("RGB Color", "frames"); //Convert image to RGB

run("Stack to Images"); //Separate stack to individual RGB images for each timeframe

selectWindow("MAX_mitosis-1-0001"); //Select the first image separated from the stack

run("Scale Bar...", "width=5 height=7 thickness=2 font=14 color=White background=None location=[Lower Right] horizontal bold hide overlay"); //Add scale bar

run("Flatten"); //Stamp scale bar on image

Note: You can also select a block of text and press Ctrl+/ to comment or remove comment status. This is very useful if you want to temporarily remove a step in your pipeline

The script is working, but there are loads of other windows still open. This is messy and confusing.

When working manually you can close individual windows with the shotcut Ctrl+W or close all open windows with Ctrl+Shift+W.

To tidy up our script we can close the unwanted windows by adding close("mitosis.tif") ;close("MAX_mitosis.tif") ;close("MAX_mitosis-1-0001") ; //close unwanted images

Note: The semicolon can also be used to separate lines of code which are actually written on the same line, as with this script to close the unwanted images.

Let's get coding!

Congratulations you've just written a program in ImageJ :)

Easy isn't it?

Before going any further let's think about the basics of what is in your script:

There are functions e.g. "run" or "selectWindow"
And there are commands between brackets and quotation marks, providing details of that function

Loads of functions exist. They will pop up in the script window as you begin typing and provide helpful guidance
A library of built in functions also exists: https://imagej.nih.gov/ij/developer/macro/functions.html

Finally, and importantly, there is a semicolon (;). This defines the end of a line and while easy to leave out, can cause a lot of issues in its absence.

Generally ImageJ deals with thee main data types:

Numbers

Can do maths with these

Strings

Defined between quotation marks ""
These can be text or numeric, but are not treated like numbers and you can't do maths on them
Note: The commands being used in our script were in quotation marks. These are strings!

Arrays

Lists of strings or numbers (or both)
We'll think about these more later

Playing with strings

Here we will write a string, which as well as a useful exercise, is a programming right of passage
Open a new script (we'll keep working on the previous one in a minute)
Type "Hello World!"; into the script editor and run
This phrase will be displayed in the Log window (sometimes this becomes buried and needs to be found via Window > Log)

You may often find it necessary to combine strings, this can be acheived by using +, e.g. "Hello" + " World!";

This can be particularly useful when editing the strings which form commands within functions

Information can also be stored as a variable for later use
Here we provide an arbitrary reference name which can be e.g.

a="Hello";

b=" World!";

c=a+b;

print(c);

Note: Once assigned to a variable, strings and numbers need to be printed out to view, using print()

Exercise 4: Putting string to work

Return to your image processing script
This is getting good, but currently we still need to save all the images at the end
An alternative would be to set a directory to save into
This can be done using getDirectory. Type it into the script and look at the options which pop up
Variants of this function will provide the adress of specific directories used by ImageJ, apart from getDirectory(string)
This allows the user to provide an address, and the string inside is simply a title given to the file browser opened
Test it on its own in a new script e.g. getDirectory("Select a directory");
To make use of this function we need to record the address of the directory selected e.g. dir=getDirectory("Select a directory");
Try this out and use print(dir); to check it's worked

Images can be saved as tiffs using saveAs("tiff", path);, where "path" is a string of the address

Add the code to set a directory to the beginning of the mitotic image processing script

Use the variable "dir" to set the path the images will be saved to

You will need to select each image in turn
Then run the saveAs function described, combining dir to a filename of your choosing which must end ".tif" e.g. saveAs("tiff",

Try to work out how to do this on your own. If you're confused, look here for some help

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