[SOLVED] Loading 3D Objects

Hello,

I'm new to KNIME. Actually I'm also new to image processing, so please forgive me my newbie questions.

Is it possible to load 3D image/object into KNIME? I have a 3D object file (.obj format file) and I can't figure it out. Is there any way to process such object in KNIME? Or maybe should I convert it into some different format file?

Best,
Joanna.

Hi Joanna,

yes, Loading 3D or even higher dimensional images is possible with KNIME.

To do so, you have to install the KNIME Image Processing Extension (see: http://tech.knime.org/wiki/install-knime-image-processing for details). If  you additionally install the ImageJ3D Viewer Extension (http://tech.knime.org/imagej-3d-viewer) then you actually can also see the Image in 3d.

Then you can use the Image Reader node to read in your file. I'm not sure if you can open .obj files, but if you can open it with for example ImageJ or FIJI then it is also possible with KNIME.

If you can't open it, you can convert it to a different format, for example .tiff.

After you opened you file, you can make a rightclick on your node and open the TableCellView. Click on your image on the left and then you see the object.

Anyway, you find a very nice introduction to KNIME Image Processing in our webinar which was recoreded this march: http://www.youtube.com/watch?v=MqSIyqmm3EU&feature=youtu.be&a.

Example workflows and more information you can find here: http://tech.knime.org/community/image-processing.

If you have any further questions, I'm happy to help you.

Christian

Hi Christian,

Thank you for your help!

It appears I need to find a way to convert this .obj file.

Best,
Joanna

Which program produces the .obj file? Is it: http://de.wikipedia.org/wiki/Wavefront_OBJ?

Then we don't support it.

Here is a list of supported file formats: http://www.openmicroscopy.org/site/support/bio-formats5/supported-formats.html

 

Yup, that's this program. To be honest I was afraid that KNIME doesn't support .obj files.

However I have another idea.

I don't know how much familiar you are with the .obj file format. The .obj file contains the coordinates of points, which allow you to reproduce the surface of a 3D object. It's more like 3D model, than 3D image. It can be saved as .txt file and those coordinates can be used to create 3D plot for example.

I need to pick few of those points and obtain their coordinates. It's impossible to do it without seeing a plot (or an object), because there are hundreds of thousands of these points. So what I need to do is to generate 3D plot, pick some points from this plot and get those points' coordinates.

I did it once using R, but it's long and laborious process. That's why I'm looking for some easier solution.

So is there any way to pick and process some points from the 3D plot? Should I install some another KNIME extension?

Regards,
Joanna

Hm, this seems very tricky. You could use the 3D Scatter Plot from the Erlwood Community Contribution, hilite the points you need and filter them afterwards using the hilite-filter mechanism on your table.

Anyway, what are you trying to do afterwards? Maybe we find a better solution :-)

Oh, it is tricky.

So I tried to use this 3D Scatter Plot but the plot is even less clear than in R. Moreover, there are so many points that I can barely rotate the plot.

My task is to pick those points from a few objects and analyze them. I'm sorry, I don't think I can tell you something more, but believe me, I really need those points. Probably I'll get back to R.

But I have to admit, KNIME is one of the most user friendly data mining software I have ever used and I'm going to use it to another purposes.

Thank you for your time and all your help!

Best,
Joanna

Good luck! If you can somehow convert the image into a BitType Tiff-format or something like that, then you could use the Interactive Annotator to mark your points ;-)
 

Greetings,

Christian