imagej 常用功能教程

ImageJ这套软件可以自动帮你你计算细胞数，也可以定量分析DNA电泳或是

Western blot条带。

step 1.首先打开软件后，开启图档

ImageJ这套软件可以自动帮你你计算细胞数，也可以定量分析DNA电泳或是

Western blot条带。

step 1.首先打开软件后，开启图档

step 2.请先做校正，选择Analyze底下的Calibrate选项，再选择校正的模式，

使用Uncalibrate OD，再按ok

按下ok之后会出现校正的图形

Step 3.在要分析的第一条(first lane)加上一个长型框(工具列第一个选项)，

再按下Analyze/Gels/select first Lane快速键(Ctr+1)，此时框架中会出现

一个号码1，之后可以移动框架到第二个lane再选择Analyze/Gels/select

second Lane快速键(Ctr+2)，当然可以一直加下去，最后按Analyze/Gels/plot

Lanes快速键(Ctr +3)。

Step 4.分析以后会出现图型表示你刚选择的框内的影像强度，此时可以看到有

几个比较高的区段，就是我们想定量的band，使用直线工具(工具列第五个选项)

先将图形中高点为有band的区域和没有band的区域分开再，使用魔术棒工具

(工具列第八个选项)点选要分析的区域。

Step 5.当我们点选分析时，在result的对话视窗会出现分析的数据，依序点

选就会出现每个band的值。

注：当我们选择分析的条带也可以是横向选取，就可以只比较相同大小的DNA

的含量，同样也可以应用在western blot或其它类似实验条带的分析上。

使用ImageJ 分析图像中的颗粒数

[] 原创教程，转载请保留此行

1，到本站资料下载-实用小工具栏目下载 ImageJ 并安装。

2，打开ImageJ并打开要分析的图片。请看演示图片。

3，把图像二值话或者设定阈值。选择 Image - Adjust -

根据提示设定你需要的阈值。这一步非常重要，关系到结果的正确性。设定阈值的标准就是把是颗粒的地

方都突出出来。示例中颗粒都被染成了红色。

4，菜单 Analyze - 自动统计结果。示例图片中有2个1像素的点都被统计出来了。

结果非常准确。

使用ImageJ 分析图像中的颗粒数

[] 原创教程，转载请保留此行

1，到本站资料下载-实用小工具栏目下载 ImageJ 并安装。

2，打开ImageJ并打开要分析的图片。请看演示图片。

3，把图像二值话或者设定阈值。选择 Image - Adjust -

#1

根据提示设定你需要的阈值。这一步非常重要，关系到结果的正确性。设定阈值的标准就是把是颗粒的地方都突出出来。示

例中颗粒都被染成了红色。

4，菜单 Analyze - 自动统计结果。示例图片中有2个1像素的点都被统计出来了。结果非常准确。

ImageJ 功能强大，其他功能请自学或者听下回分解！再见~~~

附件:

(9.26 KB)

(26.63 KB)

ImageJ 功能强大，其他功能请自学或者听下回分解！再见~~~

(22.57 KB)

(24.67 KB)

(38.38 KB)

2007/4/6 21:53

生物医学影像分析软件--ImageJ计算细

胞数

2009年04月21日 22时21分52秒 来源：未知 浏览： 522

次

相信许多朋友也许也在找一种影像软体，可以自动帮你计算细胞数，比方说常常

用使用4'-6-Diamidino-2-phenylindole (DAPI)，或是用其它的抗体在做免疫

染色(Immunohistochemistry Staining)，要如何把影像的资讯数量化呢?最常用

的就是计算染色的细胞数。那有没有软体可以自动帮你算细胞数呢?大概在90

年中就有人在做这种影像分析，在2000年左右也有不少文章介绍各实验室自己

开发的软体，也免费的提供下载。最近由猪排饭同学介绍一套软体ImageJ，是

由National Institutes of Health (NIH)所开发免费且跨平台(windows、Mac、

Linux都可用)的影像分析软体，试用一下觉得相当好用。请参考以下之教学：

step 1. 下载安装ImageJ软体: /ij/ 或

ImageJ下载

/html/protocol/ruanjianjiaocheng/2009/0421/

请依据不同作业系统选择适合的版本

step 2. 打开软体，再开启要分析的图片(File->Open)。

step 3.

设定分析影像的阈值(Image->Adjust->Threshold,或快捷键Ctr+Shift+T)

step 4.调整阈值再按set决定。

step 5.

选择analyze particle(Analyze->Analyze particle)

并且记得要选择summarize，才会有分析的结果。

step 6.

分析结果，可以看到原图像的视窗会出现电脑判读的数据，summary会显示个数

及分析影像的区域大小

8/13/2009Tutorial ImageJ

Using ImageJ to Quantify Gel Images

This is a quick tutorial abour using ImageJ to process gel images taken with the GelDoc. ImageJ is a

free program that was originally written at NIH. ImageJ is used to analyze/process all sorts of

images in biology-related research. You can use ImageJ to crop/invert/rotate/enhance your gel

images. There is even a way to quantify your bands.

Rotating/Cropping Gel Images

Open ImageJ using the shortcut on the desktop.

You can drag the image you want to open onto the ImageJ window. Once the gel image is open,

you can zoom in with "Ctrl+" and zoom out with "Ctrl-". Your gel will look something like this (see

below).

C:/…/1/10

8/13/2009Tutorial ImageJ

Now you can rotate the image in case it's crooked. Go to

Image/

You will

get the following dialog window. You can adjust the rotation angle (positive or negative values). To

make it easy, make sure that the "Preview" box is checked, that will show you how your image is

rotated, and it will also show you vertical/horizontal lines for orientation. Click OK when you're

done.

C:/…/2/10

8/13/2009Tutorial ImageJ

Now it's time to crop the gel image. Use the "Rectangular Selection" tool. After selecting the region

of interest go to

Image/Crop

to crop the below for screenshots.

Enhancing the Gel Image

This is a typical step when dealing with gel images. You need to adjust the histogram of the image.

Please make sure not to blow-out (saturate) the whites. You want to make sure your image has

enough dynamic range. Talk to me if you're confused. Anyways, you can do that with

Image/

, see the Brightness&Contrast window and the

enhancement results below. Click on "Apply" and close the menu.

C:/…/3/10

8/13/2009Tutorial ImageJ

Inverting the Image

In most cases you will want to invert the EtBr gel images for convenient viewing and economic

printing. Do this by going to

Image/LookupTables/InvertLUT

which will give you the result

shown below. You can use Brightness&Contrast enhancement once again if you wish, but this one

is good enough to move on.

C:/…/4/10

8/13/2009Tutorial ImageJ

Quantifying Gel Lanes with ImageJ

Warning - this is not going to be accurate to the percent. It works and you can put some numbers

on your results, but digital camera images are not going to be numerically as accurate as a Typhoon

scan. You need to select your lanes first. I will do horizontal selections, but you can also do vertical

selections if needed. First of all, click on the "Rectangular Selection" tool

Do a tight selection around the lane of interest. Press "Ctrl+1" to designate the first lane. Grab the

selection and drag it down to select the background (to use late for background subtraction). Press

"Ctrl+2" to designate the second lane, then if you select a third lane, you press "Ctrl+2" for any

additional lane. Once you're done, press "Ctrl+3" to plot the lane grayscale density. You can access

C:/…/5/10

8/13/2009Tutorial ImageJ

other gel-related functions in the

Analyze/Gels

menu. If you select horizontal lanes like I did here,

you will be asked whether you really want your lanes horizontal. Just say yes.

I only had two lanes - the bands of interest and the background lane. So ImageJ plots two separate

grayscale profiles. You can see that subtracting the background will really make a difference. If your

profiles look weird, please go to

Analyze/Gel/GelAnalyzerOptions

and make sure that the

"Invert Peaks" option is checked.

C:/…/6/10

8/13/2009Tutorial ImageJ

Now you will have to manually select your bands. This is done with the line select tool (press shift

C:/…/7/10

8/13/2009Tutorial ImageJ

key while drawing a vertical line). This is not as sophisticated as the Typhoon Software, but it offers

a bit more control.

Now you can identify each band by using the "Wand Tool" (see below). Click with the Wand Tool

inside each selection corresponding to a band. Then you can go to

Analyze/Gels/LabelPeaks

and

ImageJ will label each selection defined with the WandTool. There is also a "Results" window that

lists the results. Use the "Area" values and make sure to subtract the corresponding background

offset value.

C:/…/8/10

8/13/2009Tutorial ImageJ

C:/…/9/10

8/13/2009Tutorial ImageJ

Saving and Printing

At the end, please save your gel image by going to

File/SaveAs

, I would recommend saving as

TIFF or PNG (lossless). You can email the gel images to yourself. Currently there is no way to print

gels directly from the GelDoc computer.

C:/…/10/10

Gao yan

ImageJ Features



Runs Everywhere:



ImageJ is written in Java, which allows it to run on Linux, Mac OS X and Windows,

in both 32-bit and 64-bit modes.

ImageJ and its Java source codeare freely available and in the public domain. No

license is required.

Extend ImageJ by developing plugins using ImageJ's built in text editor and Java

compiler. More than 500 plugins are available.

Measure area, mean, standard deviation, min and max of selection or entire image.

Measure lengths and angles. Use real world measurement units such as millimeters.

Calibrate using density standards. Generate histograms and profile plots.



Open Source:





Plugins:





Analysis:



Installation









Linux

Mac OS X

Mac OS 9

Windows

Windows

/ij/

Download ImageJ 1.44 bundled with

32-bit Java 1.6.0_20(28MB), with 64-

bit Java 1.6.0_20(24MB; requires 64-

bit Windows) or without Java(3MB).

Open

Reads an image and displays it in a separate

window. Files must be in TIFF, GIF, JPEG,

DICOM, BMP, PGM or FITS format. Also opens

ImageJ and NIH Image lookup tables (with ".lut"

extension). Additional file formats are supported

via plugins installed in the Importsubmenu.

Subtract background

U1

幻灯片 10

U1

User, 2011/4/17

Merge channel

Scale bar



Scale bars should be present on all

publication/presentation images/movies.

It’s worth putting them in sooner rather

than later. Choose a standard scale bar size

for all your images if possible to avoid

confusion.













If you know the size of a feature (previously

applied scale bar for instance) you can use this

command to apply a calibration.

Using the line selection tool, draw a ling along

the length of the feature/scale bar.

Run the menu command “

Plugins/Spatial

calibration/Set scale

”[1].

Enter the dimensions of the object/scale bar in

the “

known distance

”box and set the units in

the

Unit of length

box.

Do not check

Global

unless you wish all your

images to have this calibration! ClickOK.

Analyze Particles and count cell



This command counts and measures objects in

binary or thresholded images. It works by

scanning the image or selection until it finds the

edge of an object. It then outlines the object

using the wand tool, measures it using the

Measure command, fills it to make it invisible,

then resumes scanning until it reaches the end

of the image or selection. Press the esc key to

abort this process. Use

Image>Adjust>Threshold

to threshold an

image.

Selection and crop

Thank you !

2011-4-19

Image J Protocol

1

1. Open Image J and, in it, open the .TIF file to be

analyzed -in this case, “”.

BE1152

1b. Optional

3

2. In the main menu, select Analyze >Calibrate.

BE1154

3. Select the Uncalibrated OD option from the

Function: dropdown box, then click OK.

5

4. A logarithmic plot should appear; move it to the side,

but do not close the window.

6

5. Go back to your .TIF image and select the Rectangle

Tool from your toolbox. Box all of the bands of interest

across all of the lanes and hit Crtl-H to bring up a

histogram.

7

6. Carefully outline the first lane with the same tool. Go

to Analyze >Gels >Select First Lane.

8

7. Drag the rectangle that you used for the first lane

over to the next, and mark it with Analyze >Gels >

Mark Next Lane. Don’t draw a new rectangle! You want

every rectangle to have the same area. Repeat until all

the lanes have been marked.

9

8. Click on Analyze >Gels >Plot Lanes. You’ll end up

with an image file with plots for each of the lanes that

you marked. The plot on top is the first lane that you

marked. Use Image >Rotate 90 Degrees Right (or

Left) and/or Image >Zoom >Out so you can see and

work with all of the plots.

BE11510

(OPTIONAL) If you have more than one band per lane,

you’ll end up with a plot for a single lane that has

multiple peaks (one for each band).

You’ll need to separate them into individual peaks with

the Line Toolas demonstrated below on another

image.

11

9. Select the Magic Wand tool and select each plot

beginning with the first. A box will appear with the Area

measurement for each plot as it is selected. The area of

that histogram plot represents the darkness of each

band in the gel.

12

10. Once you have selected each band, you can

analyze the area measurements in your spreadsheet of

choice.

13