- 1 Introduction
- 2 Recipes
- 2.1 How to get the appropriate version of Fiji running
- 2.2 How to open/import raw data
- 2.3 How to navigate through 3D or 4D data
- 2.4 How to measure angles (in 2D or 3D), distances, areas, intensities
- 2.5 How to analyze colocalization of labels
- 2.6 How to stitch together two images
- 2.7 How to view your data using volume rendering
- 2.8 How to segment objects, track them, deconvolution, filtering
- 2.9 How to export measurements for use in other programs, such as R, Matlab or Excel
- 2.10 How to plot graphs from the measurements directly
- 2.11 How to control a microscope
- 2.12 How to make simple macros/scripting (like do a given operation of whole bunch of pictures....)
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
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.
(turning, playing/making movies, projections)
How to measure angles (in 2D or 3D), distances, areas, intensities
How to analyze colocalization of labels
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)