Revision as of 09:52, 20 October 2011 by White (talk | contribs) (How to analyze colocalization of labels)


This book intends to be a users' guide for Fiji. No prior knowledge of ImageJ, programming, or "computer lingo" should be necessary to understand the recipes.


Cooks call them recipes, biologists protocols, and programmers call them HOWTOs. No matter how you refer to them, here they are:

How to get the appropriate version of Fiji running

Please see the instructions for Linux, MacOSX, Windows.

How to open/import raw data

Remark: programmers are often confused what you mean by raw data -- you talk about unprocessed data, while they refer to a certain file format.

Images come in many formats: LSM, Metamorph, Spot, CellR..... etc. Most of them can be opened by Fiji (thanks to the Bio-Formats plugin.

The easiest method is to mark the files you want to open the folder (in Finder, Explorer, Konqueror or whatever the program is called on your operating system), and drag-n-drop them onto the Fiji main window.

How to navigate through 3D or 4D data

(turning, playing/making movies, projections)

How to measure angles (in 2D or 3D), distances, areas, intensities

How do I overlay two gray images, one as red and the other as green?

Use Image>Color>Merge Channels...

TODO: screenshot, explain what "Composite" does (which is on by default...)

How to put several images into one panel

How to analyze colocalization of labels

Read this: Colocalization Analysis

How to stitch together two images

How to view your data using volume rendering

How to segment objects, track them, deconvolution, filtering

all of which 2D, 3D and 4D

How to export measurements for use in other programs, such as R, Matlab or Excel

How to plot graphs from the measurements directly

How to control a microscope

(x-y-z drive, stacks, timeseries, autofocus, find object although they have moved and keep them in the field of view between timepoints; ,maybe even get a warning in the 4th floor, when something fails at the scope in the cellar)

How to make simple macros/scripting (like do a given operation of whole bunch of pictures....)

Judith's questions

What is the secret meaning of life