"Save as movie" plugin for ImageJ

Very useful plugin:

https://sites.google.com/site/qingzongtseng/save-as-movie

Memory management in ImageJ: memory release

A few important details about how memory release/emptying in ImageJ:

• http://stackoverflow.com/questions/22912063/automatically-release-unused-memory-in-imagej-fiji

• http://fiji.sc/wiki/index.php/TrakEM2#Running_fiji_for_heavy-duty.2C_memory-intensive.2C_high-performance_TrakEM2_tasks

Create a new shortcut to a command in ImageJ/Fiji

Very useful when you frequently call a command and you want to avoid wandering around/through the command menu trees.
Go to the Plugins menu. Choose Shortcuts, then the Create shortcut... command.

Define a ROI by coordinates and size in ImageJ

Problem: I need to create a ROI in a very large 3D image (4020 x 4020 x 880) by ImageJ. The use of the mouse pointer is not so handy because it's not easy to locate the top-left vertex of the ROI at the exact wanted voxel location, due to the large size of the image.

Solution: Edit/Selection/Specify opens a plugin that allows defining manually the coordinates of the top-left vertex of the ROI, its height, width and on which slice to show you (if you are working with a stack of 2D images).

Running multiple instances of ImageJ

Multiple instances of ImageJ cannot be run, by default.

Try to double click on the ImageJ icon multiple times, after an instance of it is already opened, and the control will return to the already open instance.

To start multiple instances of ImageJ you need to

1. change a default option that allows to run a single instance listener only; you can do that under Edit -> Options -> Misc ..., where you can uncheck the box close to Run single instance listener;
2. start ImageJ by the command line with the option --allow-multiple, e.g., $ ImageJ-linux64 --allow-multiple

Set maximum memory limit in Fiji

Fiji is a "bundle version" of ImageJ, i.e., ImageJ + a lot of plugins already developed and installed.

I use it on a daily basis for my image processing/analysis tasks.

When there is need to import a sequence of images as a stack and such stack is quite big, you may need to setup a larger maximum memory limit than what it comes with the standard setup.

In order to do that, open the menu Edit -> Options -> Memory & Threads and fix the maximum memory limit.

This operation essentially writes into Fiji startup configuration file, called jvm.cfg and located within Fiji's root folder. If you open it, you can see the Java Virtual Machine option -Xmx????m, where ????m indicates the maximum memory limit expressed in MBytes.