Dear all,
I am interested in reconstruct 3D images from Z stacks with Amira but I have never used it and I cannot find any specific tutorial for this.
I explain. I acquired 3D stacks (coordinates X, Y and Z) from different tissue sections. Now I'd like to reconstruct the whole tissue by "attaching" all these stacks together.
I know it's possible in Amira but I don't know how.
Has anyone ever used Amira?
Is so, please, suggestions? or is there a protocol somewhere?
Thank you
The HelpManual/ file that is included with Amira contains useful tutorials for section alignment, segmentation and surface rendering. You might take a look at our methods in:
https://www.ncbi.nlm.nih.gov/pubmed/12746463
https://www.ncbi.nlm.nih.gov/pubmed/21138978
https://www.ncbi.nlm.nih.gov/pubmed/27884980
Dear Laura
We are using Amira for more than 10 years in our group, to create 3d models from xyz image stacks. Mainly with naturally aligned images (medical imaging), but also from non aligned stack (after slicing a specimen from histological sections).
The former is easy and Amira (like other software) generate the 3d surfaces quite easily (depending on the dataset contrast).
For the latter (non aligned images), you'll have to help Amira aligning the images by setting so-called landmarks on each images. This can be time consuming but you will eventually be able to perform then the image segmentation to get the 3d model.
I hope this helps.
In complement to my previous answer: you can normally download and use Amira for one month free of charge. And as somebody else mentioned, their tutorials are quite comprehensive.
Thank you for your answers, are very helpful.
We have Amira already installed on our campus so I ca use it.
I'll have a look at tutorials.
Thank you
Hello Laura, did you solve your problem?
I also want to use Amira to recontruct sections to 3D, but after I align the sections, I don't know how to process them to 3D model. The Amira 5.4 user guide didn't show the process clearly.
Could you please show me the next step how to process the .am file?
Thank you so much!
Hello Yingnan,
Just follow the tutorials in this order:
1. Alignment of 2D Physical Cross-Sections
2. Image segmentation
3. Surface reconstruction
an example is given in help/demos: "Geometry Reconstruction"
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