> Dear Gary,
> The images obtaines of our instrument could not be directly opened
> using any
> plugin devoted for AFM. We have a SPM-9600 Shimadzu. However, we
> can export
> as an image file. In this way, we had success to open and draw the
> 3D image
> using your suggestion (Interactive 3D surface plot). Thank you very
> much!
> At this moment, we are trying to segment objects in such image in
> order to
> obtain the absolute volume of each object dispersed in the surface.
> For each
> image we can see dozens of the irregular particles we want measure.
> Have you
> some suggestion to perform this?
> Thanks in advance,
> Luciano
>
>
> 2008/3/12, GCH <
[hidden email]>:
>>
>> Hi,
>>
>> If I remember correctly, the problem with some AFM images is that
>> they may be composed of several channels. If your images are ascii,
>> 512x512 pixels the File/Import/Text image... shuodl do the job.
>> Somewhere I also have a macro (provided mostly by Wayne) that I used
>> to open AFM images (single or series within a folder) automatically.
>> I can send it to you in a separate email if necessary.
>>
>> Once you open the images you can use the Interactive 3D surface plot
>> by Kai Uwe Barthel (
http://rsb.info.nih.gov/ij/plugins/surface->> plot-3d.html) to render and visualize the surface. It works great!
>>
>> You can also use the SurfCharJ to characterize and describe the
>> surface topography.
>>
http://www.gcsca.net/IJ/SurfCharJ.html>>
>> I hope this helps,
>>
>> Gary.
>>
http://www.gcsca.net>>
>>
>>
>>
>>
>> On Mar 12, 2008, at 6:02 PM, Joachim Wesner wrote:
>>
>>> Hi Luciano, what David is refering to is that "text image" will
>>> take your
>>> single file and create a 2D image where intensity (grey) value
>>> represent
>>> height (Step 1), starting from that you likely
>>> can use SurfaceJ to create a true 3D representation of your object
>>> (s).
>>> (Step 2)
>>>
>>> However, as I mentioned in that other post, if one considers a
>>> simple fully
>>> convex closed sphere/cell, one will even in the simplest case get
>>> TWO z
>>> values for each x and y inside the projection of that
>>> cell (upper and lower surface), the more folded the surface the more
>>> nonunique entries (x,y). Then text import will not work!? Is that
>>> the case
>>> with your data?
>>>
>>> Mit freundlichen Grüßen / Best regards
>>>
>>> Joachim Wesner
>>>
>>>
>>>
>>>
>>> David Hovis
>>> <
[hidden email]>
>>> Gesendet
>>> von: An
>>> ImageJ Interest
[hidden email]
>>>
>>> Group Kopie
>>> <
[hidden email].
>>>
>>> GOV> Thema
>>> Re: 3D Display
>>>
>>> 12.03.2008 17:22
>>>
>>>
>>> Bitte antworten
>>> an
>>> ImageJ Interest
>>> Group
>>> <
[hidden email].
>>> GOV>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Mar 12, 2008, at 12:16 PM, Luciano Silva wrote:
>>>
>>>> Dear Leon,
>>>> In our situation, we have the 3D coordinates in order to be plotted
>>>> aiming
>>>> future segmentation of 3D objects distributed on the surface. We
>>>> are
>>>> not
>>>> looking for a plugin that is able to render 3D images using color
>>>> intensity.
>>>> Our data are already with X, Y, and Z directions of the surface. We
>>>> have
>>>> these data as a matrix X/Y of defined dimension and for which any
>>>> value is
>>>> the Z (height). In this way, your suggestion is not aimed to solve
>>>> this.
>>>> Thanks in advance,
>>>> Luciano
>>>
>>> I'm going to repeat myself:
>>>
>>> File -> Import -> Text Image...
>>>
>>> --David
>>>
>>>
>>>
>>> ____________________________________________________________________
>>> __
>>> This email has been scanned by the MessageLabs Email Security
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>>> For more information please visit
http://www.messagelabs.com/email>>> ____________________________________________________________________
>>> __
>>>
>>>
>>
>
>
>
> --
> Luciano