Hi,
I have few SEM images from a sample which was continuously sliced and imaged. Now I need to align them and construct a 3D image. Most of softwares ask to save data in special formats. But I can only saved SEM images.
Is this sufficient to construct 3D tomogram at the end? I know the space of each plane where each image obtained.
Thanks
Thanks John. I will try MIRAR, awaiting for the trial key. :)
Thought of attach few images to your website, but it allows only one image.
If you can do a demo, that will be great!
Cheers.
Chaturanga
You should try using TrakEM in the FIJI distribution of ImageJ. (it's free, and good)
http://fiji.sc/
Thanks Maththew. I am tring, but did not work so far. That is why I am looking for some other possible tools.
Cheers.
Hello,
The stack reg plugin for ImageJ works for colleagues of mine doing SBF-SEM as a primary coarse alignement.
Stack reg is a function in image J (/FIJI) that does a pretty bang up job of aligning the slices. It is the volume viewing after which can be a challenge.
Did you do your slice and image in QUT? UQ has a good Scios operator who may be able to help you.
Hi Matthew & William,
I have aligned images using fiji. MIPAR is handy as well.
3D visualising is challenging due to the nature of sample and images. Bit hard to define boundaries.
Yes, we have used Scios in UQ to get data.
I think that UQ have access to the Aviso software. It is the FEI software for 3d visualisation, it is fairly simple and very powerful. (unfortunately, also expensive). Maybe have a chat to the UQ group about using that software.
Otherwise, FIJI.
1. Stackreg
2a. Volume viewer (simple, and useful) or
2b. TrackEM - more time consuming. You basically colour in the sections that you want to visualise on each layer. (There are some good tutorials on the FIJI website on how to use TrackEM)
Thanks Matthew. I was tring TrackEM2. Will try volume viewer. :)
Hi Chiththaka,
another software which can do this really well is Imod (University of Colorado). There is an option to align series of images and also it allows you to do segmentation. You will just need to convert your tifs to mrc file, which is easy (command tif2mrc).
Best wishes,
Petr
Hi John,
Had a look at the mipar website, and it looks to be quite good! Am going to install it now (the activation key has come through) and give it a go.
Thanks very much indeed Matthew. Please contact me any time for any needs. It is growing rapidly and there will be many improvements (stability and functionality) in the next releases. A second pre-release of beta.7 will hopefully be out tomorrow so I'll be sure to include you in the pre-release list. Hope you have a smooth install and pleasant first experience.
Cheers,
John
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