eDigitizer user guide
As a researcher, you may encounter the following situations from time to time. You need to get original data for a graph published in a scientific paper. The simple way is to use a ruler and estimate the value of each data point by eye. If you want to get the data more accurately, you have to turn to digitization software. Back to 2002, I wrote a MATLAB program that can do the job. Unfortunately, you have to own a copy of MATLAB to use the program. As inquiries increase recently, the eDigitizer is implemented in the .NET environment. There is no MATLAB required. Now the brand new implementation can run under Windows with .Net framework version 2 installed. In addition. The following lists it main features.
- Zoom and rotate images
- Test the orthogonality of axes
- Digitize axes
- Digitize data points
- Save digitized data to a text file
Get eDigitizer
Visit http://www.sunfinedata.com/graphing/edigitizer/ to download a copy of the application. This is a green software. You do not need to install it. Just expand the downloaded zip file to a folder and click the executable file – edigitizer-net2.exe. Since it need Microsoft .NET framework 2.0 runtime library, you have to install .Net framework 2.0 runtime redistribution package from the Microsoft web site.
Launch eDigitizer
First launch eDigitizer by double clicking it. You have to find the program in your hard disk by using Windows explorer or similar applications. Figure 1 shows the main window of the eDigitizer.
Figure 1
There are two functional area in eDigitizer’s main window. On the left side is a fixed area that houses all function commands. First functional block is related to image processing, such as load, zoom, rotate, restore and save image. The second functional block is related to digitizing X and Y axes and testing perpendicularity of them. The last functional block includes functions to digitize series. You can digitize as many series as you want. All data will be stored in text file. On the right side includes a zooming area with multiple tabs, image tab, graph tab and data tab. It takes the major portion of the main window. The size of this area changes with the eDigitizer window. If you move the mouse cursor to this area, the cursor changes to a big blue cross. That can help users to locate points on the screen. Before you load any image to the system, these tab areas have nothing. Next step is loading image.
Load image
Loading an image is pretty simple. Just click “Browse” button on the top of left panel and an “Open an image” dialog window will pop up (Figure 2). You can navigate to the folder where images are stored and select one to open.
Figure 2
Once the selected image is loaded, the main window looks like Figure 3.
Figure 3
Digitize axes and test perpendicularity
Now you can directly click “Test” button in the Axes frame to test the orthogonality of the axes. Move the mouse cursor to the graph and it changes to the big blue cross. You have to sample three points (the origin, one point on X axis and one point on Y axis in sequence, Figure 4) in the coordinates.
Figure 4
Click the origin, one point on X axis and one point on Y Axis sequentially, and then you will see the Theta (θ) and Alpha (α) values in the Axes frame of the left panel (refer to Figure 3). Figure 5 shows the definition of the two angles. If the alpha value is less than 1 degree and theta is around 90 degree. The orthogonality of the axes is good. You can directly digitize data points without rotation of the image. Otherwise, you have to rotate the image based on the alpha value you got in this step.
Figure 5
Next step is digitizing X and Y axes. Click X or Y button in Axes frame. The two textboxes below the buttons will change to “Name/Unit” and “Values”. What you need to do is enter the variable name and unit of X or Y axes in the first textbox and enter a comma separate values based on you actual situation into the second textbox. For the sample image we see in Figure 3, we have the following:
X axis: Name/Unit: Time (Hour); Values: -12, 0, 12, 24, 36, 48, 60, 72 Y axis: Name/Unit: mRNA; Values: 0, 0.5, 1.0
After you enter the pair for X axis, you should click “Collect” button to digitize the points in X axis. You have to digitize the points in the same order as you enter them in the Values textbox. The application will know when you finish the digitization based on the number of values you entered in the Values textbox. Once all points are digitized, there will be linear equation with R2 value shown up just above the “Collect” button. For this situation, the intercept of the linear equation is -21.55 and the slope is 0.24 with a R2 of 1.0 (See Figure 6)
Figure 6
You can follow the same step to digitize the three points on Y axis.
Digitize series
Now we are ready to digitize our first series. Let’s pick “wt(col)” line to demonstrate the process.
- Enter “wt(col)” in the Name textbox in the Series frame
- Click “Collect” button
- Move cursor to image and it will change to a big blue cross
- Move the big blue cross to the center of the first open square on the left of the image and click it
- Move the big blue cross to the next open square and click it, repeat this step until you complete the last open square on the right side of the image
- Click “Commit” button in the Series frame. Note: before digitizing, this button is called “Collect”.
- Switch to “Graph” tab, you can see the digitized series like Figure 7
- Switch to “Data” tab, you can see the digitized data like Figure 8
Figure 7
Figure 8
Congratulations! You have completed your first digitization. You can click “Save” button in the Series frame to save your results to a file for late use. Is it simple? Yes, it is pretty simple. You can digitize as many series of you want and save them into one text file.
[...] eDigitizer user guide Posted 2009/08/18 by Zhanshan Dong. Comments and trackbacks are open. Follow the comments feed. Filed under: Data analysis Graphing Tagged with: .NET, eDigitizer, graph, Windows. [...]