ImageJ用户指南：免费图像处理软件深度解析

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"ImageJ用户指南，由美国国立卫生研究院开发的免费图像处理软件，具有丰富的超文本链接，可离线查看和搜索。该指南作为ImageJ文档资源的补充，鼓励用户和开发者贡献更新内容。最新版本可在指定网址获取。" ImageJ是一款由美国国立卫生研究院(NIH)研发的免费图像处理软件，它被广泛用于科研和教育领域，具有强大的图像分析功能。此用户指南是ImageJ的重要参考资料，涵盖了从基础操作到高级应用的多个方面。 1. **ImageJ的功能特点**：在Version 1.43中，该软件实现了多种特性，包括但不限于图像处理、分析、测量、插件扩展等。具体实现的功能可以通过指南的“Features Implemented in v1.43”部分详细了解。 2. **安装与维护**：ImageJ的安装过程简单，指南中提供了详细的步骤。同时，关于如何保持软件的最新状态和进行常规维护，也有相应的指导。 3. **使用指南**：ImageJ的用户界面友好，但为了充分利用其功能，用户需要了解如何使用快捷键和修改键(“Shortcuts and Modifier Keys”)，以及如何查找和执行命令(“Finding Commands”)。 4. **撤销与重做**：ImageJ支持撤销和重做操作，这对于实验性的图像编辑特别有用，允许用户纠正错误或尝试不同的处理方法。 5. **图像类型与格式**：ImageJ能够处理多种类型的图像，包括灰度图像、彩色图像，并支持多种图像格式。指南详细解释了不同图像类型的特点，如“Image Types and Image Formats”。 6. **堆栈、虚拟堆栈和超堆栈**：ImageJ的“Stacks, Virtual Stacks, and Hyperstacks”特性允许用户处理多帧图像，比如时间序列或多通道图像，这对于生物学和医学研究尤其有价值。 7. **彩色图像处理**：对于彩色图像，ImageJ提供了丰富的处理工具，包括颜色分离、色彩调整和色彩空间转换，这部分在“Color Images”章节中有详细介绍。 8. **获取帮助**：除了用户指南，ImageJ还提供了其他帮助资源，如在线论坛、邮件列表和社区支持，用户在遇到问题时可以找到多种求助途径。 9. **持续更新与贡献**：由于ImageJ的持续开发，该指南始终处于未完成的状态，鼓励所有用户和开发者参与到更新和完善中来，共同构建更全面的文档。 ImageJ用户指南是学习和掌握这款强大图像处理软件的必备资料，无论你是初学者还是高级用户，都能从中受益。通过深入学习和实践，你可以利用ImageJ进行复杂的图像分析和处理任务，满足科学研究和专业图像编辑的需求。

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 com-

mand is much more eﬀective than a general Re: Problem

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

thread

ﬁles. Use, e.g., a ﬁle hosting service instead

(d) Edit replies – You should include only the minimum content that is nec-

essary to provide a logical ﬂow from the question to the answer, i.e., quote

only as much as is absolutely necessary and relevant.

Part II

Working with ImageJ

For a detailed description of all ImageJ menus and toolbar buttons (most are self-

explanatory), have a look at Parts III on page 27 and IV on page 37.

6 Shortcuts and Modiﬁer Keys

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 document.

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.

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

cuts are listed throughout ImageJ menus. Similarly, in this 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 explic-

itly 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 text editor

(page 22), 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 or Ctrl Shift ⇑ I

if Require control key for shortcuts is checked. The full list of ImageJ shortcuts can be

retrieved at any time using the Plugins . Utilities . List Shortcuts... command. This list is

also available on page 159.

# 1. Frontmost Window and Windows Activation

In ImageJ, all operations are performed on the active (frontmost) image (which

has its title bar highlighted). If a window is already open it will activated when its

opening command is re-run, e.g., if the B&C window is already opened pressing

its keyboard shortcut Shift ⇑ C will activate it.

In addition, Pressing ←- on any image will bring the ImageJ window to the

foreground.

Search...

Plugins . Utilities . Search... searches recursively for a particular string (case sensitive or

not) contained in the ﬁle names or ﬁle contents in a chosen folder or in ImageJ/macros

folder if Search Macros Folder is checked.

Since most macros (.txt, ijm), scripts (.js) and plugins source (.java) ﬁles contain cir-

cumstanced information as commented code, you can use this utility to retrieve ﬁles

not only related to a image processing routine (e.g., background or co-localization) but

also topics related to a certain scientiﬁc context such as radiogram, cell or histology.

Indeed, the ImageJ source ﬁles contain detailed annotations useful to both developers

and regular users that want to know more about ImageJ routines and algorithms.

The results are displayed in the Log window. If the Search Contents option is checked, the

line number where the string was found is displayed. In the Log window, double click on

a ﬁle path to open that ﬁle in an editor window. There is an option to search the macros

folder and also an option to search the ImageJ source code if it has been downloaded

(from rsb.info.nih.gov/ij/download/src/) and extracted into the ImageJ folder. This

command runs the macro Search in ij.jar.

See also: Appendix A Keyboard Shortcuts and SourceCodeRetriever, a macro that searches

for a menu entry and tries to retrieve the java source ﬁle of the respective plugin

8 Undo and Redo

Probably the ﬁrst thing you will notice is that ImageJ does not have a undo/redo buﬀer.

Undo (Edit . Undo [z]) is currently limited to the most recent image editing / ﬁltering

operation. With time you will appreciate that this is necessary to minimize memory

overhead. If you cannot recover from a mistake, you can always use File . Revert [r] to

reset the image lo its last saved state. For selections, Edit . Selection . Restore Selection

[E] can be used to recover any misdealt selection.

In ImageJ the equivalent to ‘Redo’ is the Process . Repeat Command [R], that re-runs the

previous used command (skipping Edit . Undo [z] and File . Open... commands).

See also: Plugins . Utilities . Reset..., Multi Undo plugin

# 2. Limitations of Edit . Undo [z]

Edit . Undo [z] and File . Revert [r] are not available on operations performed on

entire stacks.

9 Image Types and Image Formats

Digital Images are two-dimensional grids of pixel intensities values with the width and

height of the image being deﬁned by the number of pixels in x (rows) and y (columns)

direction. Thus, pixels (picture elements) are the smallest single components of images,

holding numeric values – pixel intensities – that range between black and white. The

characteristics of this range, i.e., the number of unique intensity (brightness) values that

can exist in the image is deﬁned as the bit–depth of the image and speciﬁes the level of

precision in which intensities are coded, e.g.: A 2–bit image has 2

= 4 tones: 00 (black),

01 (gray), 10 (gray), and 11 (white). A 4–bit image has 2

= 16 tones ranging from 0000

(0) to 1111 (16), etc.. In terms of bits per pixel (bpp), the most frequent types of images

that ImageJ deals with are:

8–bit Images that can display 256 (2

) gray levels

16–bit Images that can display (2

) 65, 536 gray levels

32–bit Images that can display (2

) 4, 294, 967, 296 gray levels. These are ﬂoating

point grayscale images. In computing, ﬂoating point describes a system for

representing numbers that would be too large or too small to be represented

as integers. Indeed, in 32–bit images a pixel can have any intensity value

including NaN (Not a Number).

RGB Color Images that can display 256 values in the Red, Green and Blue channel.

These are 24–bit (2

3×8

) images. RGB color images can also be 32–bit

color images (24–bit color images with additional eight bits coding alpha

blending values, i.e., transparency).

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