Although this group of post is not valuable to many individuals, it may save a handful of people hundreds of hours. You may want to know all the information that this tutorial provides or just a small portion. I have broke it up by software packages so that you have points to jump in.
Part 1. Using ImageJ to add scale bars to a large number of photos at once. (current document)
Part 2. Using Metamorphose to manipulate files names into usable captions on photos.
Part 3. Batch adding captions or watermarks to photos based on file name. In addition we can batch crop in this step.
BEFORE YOU START THESE TUTORIALS MAKE BACKUPS OFF ALL OF YOUR PHOTO FOLDERS YOU PLAN TO USE.
The following tutorials will require the use of these software packages.
ImageJ: Is the photo editor we will use to generate scale bars.
Métamorphose: A File -n- Folder renamer. This program is used to manipulate filenames into usable captions (Use metamorphose 2 beta).
IrfanView: Photo Editor/Viewer. The program what will be used to batch caption and crop images.
Part 1 – ImageJ batch adding scale bars to images:
ImageJ is a useful tool for adding scale bars to images without much effort, but after extensive searching I was unable to find a script that would add scale bars to large groups of images. Most of the time when you take photos on a microscope or on a tripod, the scale is the same among that group of photos.
Step 1: Getting ready for Imagej
1. Group your image files into folders where all have identical resolution and scale.
Note: you can get away without doing the step above, but it makes finding errors much more difficult.
Step 2: Setting up the scale in ImageJ (You really only do this step the first time you do this process. After that you should have the macro saved)
I am not going to show you how to set up the scale in imagej because other people already have good tutorials up, but you will need to know how to do this step to edit my macro code. I sort of assume that since you found my page you already know how to set the scale in imagej, but if not to a look at these links.
Pre-create the directories you plan to use to save your photos to(imagej cannot make them).
You will change the save path in this line “saveAs(“Tiff”, “C:\\test\\40x\\”+title);”
Step 4 Editing macros and moving them to the macro directory:
The code is provided below, but just download the example here and use your favorite editor to make modification.
// Applies a scale bar to images taken with the microscope at current camera settings.
// You will change the distance and known values based off scale information obtained in the links above.
run(“Set Scale…”, “distance=746.04 known=1000 pixel=1 unit=um global”);
// This area grabs all the images that you currently have open an starts applying scale bars
for (i=0;i selectImage(i+1);
// used to keep the file name
title = getTitle();
// You will want to change the following line to reflect the look and location of you scale bar
run(“Scale Bar…”, “width=400 height=8 font=50 color=Yellow background=Black location=[Lower Right] bold”);
// Your might want to change the save type in this line to JPG. (we convert to JPG later in this tutorial)
To save time you will want to make a macro of each file resolution you may encounter. For example I have one for 40x, 100x, 200x, and 400x. In each I change the values in “run(“Set Scale…”, “distance=746.04 known=1000 pixel=1 unit=um global”);” and “saveAs(“Tiff”, “C:\\test\\40x\\”+title);” Other than that you can basically leave it alone.
Save all your files to the default macro folder in imagej:
My path is C:\Program Files (x86)\ImageJ\macros (Your path is likely different as imagej dose not typically install into the regular programs directory. )
Step 5 (Back to the regular stuff) Installing and using the macro:
Grab all the photos of the same scale and resolution that I had you folder up in step 1, and drag them an instance of imagej
Then you need to install the macro that will work with the files you have open.
When you click open it will just close the window. Fear Not
Click the macro to run it. You should start seeing photos closing. Depending on the speed of your computer you might see the scale bars being added.
The current save directory is C:\test\40x with the 40x macro. You can change it to whatever you like with any text editor. Just make sure to install the macro again if you make any changes to the text.
The macro will work for several photos at a time, but you will need to run the macro several times to get through a large group of images. I am not sure why this happens. The closer you get to completing the group of images the fewer images it will add the scale bar too. I have a feeling it has something with java trying to hyperthread, but I will take just a few clicks for hundreds of photos over thousands of clicks.
Once you have run the macro enough times all the images should be closed and resaved as tiff files with scale bars in C:\test\40x.
The first time you instal the macros you probably won’t save much time, but if it is something you need to do often you will shave off hours. In addition you look like a rock star if you are dealing with time sensitive information.