ImageJ用户指南：最新1.46r版详解与开发资源

ImageJ

user-guide

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Getting Help ImageJ2

2.3 ImageJ2

ImageJDev is a federally funded, multi-institution project dedicated to the development of

the next-generation version of ImageJ: “ImageJ2”. ImageJ2 is a complete rewrite of ImageJ,

that includes the current, stable version ImageJ (“ImageJ1”) with a compatibility layer so that

old-style plugins and macros can run the same as they currently do in ImageJ1. Below is a

summary of the ImageJDev project aims:

–

To create the next generation version of ImageJ and improve its core architecture based

on the needs of the community.

– To ensure ImageJ remains useful and relevant to the broadest possible community, main-

taining backwards compatibility with ImageJ1 as close to 100% as possible.

– Expand functionality by interfacing ImageJ with existing open-source programs.

– To lead ImageJ development with a clear vision, avoiding duplication of eﬀorts

–

To provide a central online resource for ImageJ: program downloads, a plugin repository,

developer resources and more.

Be sure to follow the ImageJ2 project news and the ImageDev blog for updates on this exciting

project.

3 Getting Help

3.1 Help on Image Analysis

Below is a list of online resources (in no particular order) related to image processing and

scientiﬁc image analysis, complementing the list of external resources on the IJ web site.

Ethics in Scientiﬁc Image Processing

– Online learning Tool for Research Integrity and Image Processing

This website, created by the Oﬃce of Research Integrity, explains what is appropriate in

image processing in science and what is not.

– Digital Imaging: Ethics (at the Cellular Imaging Facily Core, SEHSC)

This website, compiled by Douglas Cromey at the University of Alabama – Birmingham,

discusses thoroughly the topic of digital imaging ethics. It is recommended for all scientists.

The website contains links to several external resources, including:

What’s in a picture? The temptation of image manipulation (2004) M Rossner and

K M Yamada, J Cell Biology 166(1):11–15, doi:10.1083/jcb.200406019

2. Not picture-perfect (2006), Nature 439, 891–892, doi:10.1038/439891b.

Scientiﬁc Image Processing

– What you need to know about scientiﬁc image processing

Simple and clear, this Fiji webpage explains basic aspects of scientiﬁc image processing.

5 Last updated: 2012/10/02

Getting Help Help on ImageJ

– imagingbook.com

Web site of Digital Image Processing: An Algorithmic Introduction using Java by Wilhelm

Burger and Mark Burge [

]. This technical book provides a modern, self-contained, intro-

duction to digital image processing techniques. Numerous complete Java implementations

are provided, all of which work within ImageJ.

– Hypermedia Image Processing Reference (HIPR2)

Developed at the Department of Artiﬁcial Intelligence in the University of Edinburgh,

provides on-line reference and tutorial information on a wide range of image processing

operations.

– IFN wikipage

The Imaging Facility Network (IFN) in Biopolis Dresden provides access to advanced

microscopy systems and image processing. The website hosts high quality teaching material

and useful links to external resources.

– stereology.info

Stereology Information for the Biological Sciences, designed to introduce both basic and

advanced concepts in the ﬁeld of stereology.

See also: ImageJ Related Publications on page 174

3.2 Help on ImageJ

Below is a list of the ImageJ help resources that complement this guide (see Guide Formats).

Speciﬁc documentation on advanced uses of ImageJ (macro programming, plugin development,

etc.) is discussed in Extending ImageJ.

1. The ImageJ online documentation pages

Can be accessed via the Help . Documentation. . . command.

2. The Fiji webpage:

http://ﬁji.sc/

3. The ImageJ Information and Documentation Portal (ImageJ wikipage):

http://imagejdocu.tudor.lu/doku.php

4. Video tutorials on the ImageJ Documentation Portal and the Fiji YouTube channel:

http://imagejdocu.tudor.lu/doku.php?id=video:start&s[]=video and http://www.youtube.

com/user/ﬁjichannel. New ImageJ users will probably proﬁt from Christine Labno’s video

tutorial.

5. The ImageJ for Microscopy manual

http://www.macbiophotonics.ca/imagej/

6. Several online documents, most of them listed at:

http://imagej.nih.gov/ij/links.html and http://imagej.nih.gov/ij/docs/examples/

7. Mailing lists:

(a) ImageJ — http://imagej.nih.gov/ij/list.html

General user and developer discussion about ImageJ. Can be accessed via the Help

Mailing List. . . command. This list is also mirrored at Nabble and Gmane. You may

ﬁnd it easier to search and browse the list archives on these mirrors. Specially useful

are the RSS feeds and the frames and threads view provided by Gmane.

6 Last updated: 2012/10/02

Getting Help Help on ImageJ

(b) Fiji users — http://groups.google.com/group/ﬁji-users

For user discussion speciﬁc to Fiji (rather than core ImageJ).

For developer discussion speciﬁc to Fiji.

(d) ImageJ-devel — http://imagejdev.org/mailman/listinfo/imagej-devel

For communication and coordination of the ImageJDev project.

(e) Dedicated mailing lists for ImageJ related projects

Described at http://imagejdev.org/mailing-lists .

Using Mailing-lists

If you are having problems with ImageJ, you should inquiry about them in the appropriated list.

The ImageJ mailing list is an unmoderated forum subscribed by a knowledgeable worldwide

user community with

≈

2000 advanced users and developers. To have your questions promptly

answered you should consider the following:

Read the documentation ﬁles (described earlier in this section) before posting. Because

there will always be a natural lag between the implementation of key features and their

documentation it may be wise to check brieﬂy the ImageJ news website (Help

ImageJ

News. . . ).

Look up the mailing list archives (Help

Mailing List. . . ). Most of your questions may have

already been answered.

If you think you are facing a bug try to upgrade to the latest version of ImageJ (Help

Update ImageJ. . . ). You should also check if you are running the latest version of the Java

Virtual Machine for your operating system. Detailed instructions on how to submit a bug

report are found at http://imagej.nih.gov/ij/docs/faqs.html#bug.

Remember that in most cases you can ﬁnd answers within your own ImageJ installation

without even connecting to the internet since the heuristics for ﬁnding commands or writing

macros have been signiﬁcantly improved in later versions (see Finding Commands and

Extending ImageJ).

5. As with any other mailing list, you should always follow basic netiquette, namely:

(a)

Use descriptive subject lines – Re: Problem with Image>Set Scale command is much

more eﬀective than a general Re: Problem.

(b) Stay on topic – Do not post oﬀ-topic messages, unrelated to the message thread.

(c)

Be careful when sending attachments – Refrain from attaching large ﬁles. Use, e.g., a

ﬁle hosting service instead.

(d)

Edit replies – You should include only the minimum content that is necessary to

provide a logical ﬂow from the question to the answer, i.e., quote only as much as

absolutely necessary and relevant.

7 Last updated: 2012/10/02

Part II

Working with ImageJ

This part introduces some basic aspects of ImageJ so that you can use the software more

eﬃciently. It also introduces some important terms and concepts used throughout this guide.

You may skip it if you already use the program eﬃciently and are familiar with terms such

as Virtual Stacks, Hyperstacks, Pseudocolor Images, Color Composite Images or Composite

Selections.

4 Using Keyboard Shortcuts

You’ll learn more and more shortcut keys as you use ImageJ, because (almost) all shortcuts

are listed throughout ImageJ menus. Similarly, in this guide each command has its shortcut

key listed on its name (ﬂanked by square brackets). Please note that the notation for these

key-bindings is case sensitive, i.e., Shift-modiﬁers are not explicitly mentioned (a capital A

means Shift–A) and assumes that Require control key for shortcuts in Edit

Options

Misc. . .

is unchecked (i.e., except when using the IJ Editor or the Text Tool, you won’t have to hold

down the Control key to use menu shortcuts). For example, the command Edit

Invert [I] can

be evoked by

Shift I

Ctrl Shift I

if Require control key for shortcuts is checked. The

full list of ImageJ shortcuts (see Keyboard Shortcuts) can be retrieved at any time using the

Plugins . Utilities . List Shortcuts. . . command.

There are three modiﬁer keys in ImageJ:

Control

(

Command Key

on Apple keyboards) Denoted by ‘Ctrl’ or

Ctrl

in this document.

Although a control key is typically present on Apple keyboards, on a Macintosh

computer running ImageJ the Command key

Cmd

replaces the functionality of

the Control key of other operating systems. For sake of simpliﬁcation, ‘Ctrl’ will

always refer to both throughout this guide.

Shift Denoted by ‘Shift’ or

Shift

in this document.

Alt

Denoted by ‘Alt’ or

Alt

in this document. This is also the ‘Option’ or ‘Meta’ key on

many keyboards. In ImageJ, it is also used to type special unit symbols such as

(

Alt M

) or Å (

Alt Shift A

See also: Keyboard Shortcuts, Plugins . Shortcuts .

5 Finding Commands

Navigating through the extensive list of ImageJ commands, macros and plugins may be quite

cumbersome. Through its built-in Command Finder / Launcher[

], ImageJ oﬀers an expe-

dite alternative that allows you to retrieve commands extremely fast: Plugins

Utilities

Find

Commands. . . [l].

In addition, ImageJ features a ﬁnd function that locates macros, scripts and plugins source

(

.java

) ﬁles on your computer: the Plugins

Utilities

Search. . . command. Because most

of IJ source ﬁles contain circumstanced comments, you can use this utility to retrieve ﬁles

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