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Tue, 11/16/2010 - 04:33 am

Hi everyone, I am a very very beginner of Igor. I had a .ibw file, which should be from an AFM experiment. Could any one just explain a little bit how I could get the image from this file? I tried "Data"---"load data"------"load igor binary", then it seems nothing has happened afterwards. I did not see any image. Could some one help me? Thank you very much.
The data ibw should be loaded into Igor Pro if you have done the procedure you described.
You can then plot the data as an image by choosing New>Image Plot... from the Windows menu.

A

November 16, 2010 at 05:27 am - Permalink

Thank you so much. Now I can open the image, and try to analyze it.

November 16, 2010 at 06:44 am - Permalink

Right click on the image in the image plot. On the menu that appears select, "Modify Image Appearance". In the Modify Image Appearance dialog, edit the boxes for "First Color at Z=" and "Last Color at Z=" so that the details of your image can be seen. These parameters control the range of z values over which your image is displayed. Your image likely contains a few extreme pixel values that are driving the scaling values such that most of the image appears black.

November 16, 2010 at 06:46 am - Permalink

Thanks a lot. Problem solved. I think my last question would be how to analyze the z values along a line?

November 16, 2010 at 07:00 am - Permalink

bao wrote:
Thanks a lot. Problem solved. I think my last question would be how to analyze the z values along a line?


Take a look at the ImageLineProfile operation or ImageTransform with the getbeam method.

November 16, 2010 at 07:28 am - Permalink

it did not work as I want.....i have opened an old experiment file, and it contains some "sections" dialog, like in the attached image. From where can I open and operate this dialog? Thanks.
kkk.jpg

November 16, 2010 at 07:57 am - Permalink

bao wrote:
...i have opened an old experiment file, and it contains some "sections" dialog, like in the attached image. From where can I open and operate this dialog? Thanks.


This looks like a feature added through a procedure; it does not look like any built-in capability that I am familiar with. I can't find anything like this after searching the Wavemetrics Procedures folder or looking through example experiments (on the file menu). Perhaps someone in your group programmed it?

With this old experiment file open, you should look at the Windows>Procedure Windows menu item and see if any of the procedure files give you a clue. The programmer may have added a custom menu or added an item to one of the standard menus. For example, most graphing capabilities are available on the Windows menu, that is a logical location to add new graphing features.

I did a little more digging and have some additional information. I have edited my original response.

I also do AFM and have an Asylum MFP3D, which I assumed you had when I saw your opening question in this thread. The graph shown in your image is identical to a feature in their software. This capability is added by their custom programming. If you look at the menu item Windows>Procedure Windows in your Asylum control program, you will find a procedure file called "Sections"; this is likely the source for that capability. You could contact Asylum to see if they will provide a version that isn't tied to their package. Alternatively, the software license from Asylum permits you to install their AFM software on another computer for offline analysis.

November 16, 2010 at 10:42 am - Permalink

The ImageLineProfile operation can be used from the command line/inside a function. However, if you are getting started the inbuilt image analysis package is much easier to get acquainted with.

Select the Menu items: Analysis -> Packages -> Image Processing. A new menu appears, called Image. In that menu item are lots of good image analysis techniques, one of which is image line profiles. This allows you to make a line section of arbitrary width through an image.

November 16, 2010 at 03:01 pm - Permalink

bao wrote:
Thank you all.....I tried the imagelineprofile, but it seems to just give a blank graph?


I tried Image Line Profiles from the Image Processing package with an image plot opened and had the same result as bao. For me, the debugger window opens. It seems that the ImageLineProfile wave reference is null. This was for an image with 2 planes. I also tried this on an RGB image and it worked correctly. See attached file.
Macbeth.jpg

November 17, 2010 at 07:06 am - Permalink

When you initialise the imagelineprofile procedure you should already have an image open. The analysis is initialised to the top image.

November 17, 2010 at 01:35 pm - Permalink

andyfaff wrote:
When you initialise the imagelineprofile procedure you should already have an image open. The analysis is initialised to the top image.


True. Even so, there appears to be a problem (or I'm missing something -- likely) if the array displayed in the target image has other then 1 or 3 planes. Anyway this is my conclusion after a brief bit of testing this morning.

November 17, 2010 at 06:05 pm - Permalink