[Neuroimaging] 3d registration for data fusion in material science

Alexis Roche alexis.roche at gmail.com
Fri Aug 21 13:03:48 CEST 2015


Hi Gael,

Beside the stuff in dipy that Elef mentioned, there is another brain image
registration package that has slowly developed over the years, and could be
useful to you (although it still crucially lacks documentation):

https://github.com/nipy/nireg

This is rigid/affine registration only for the time being and has a BSD
license too.

Best,

Alexis

On Fri, Aug 21, 2015 at 9:57 AM, GORET Gael 246279 <Gael.GORET at cea.fr>
wrote:

> Hi all,
>
>
>
> Thanks for your quick replies,
>
> This project is just starting, and there is not too much materials …
>
> However, to answer your questions, I just have created a public repo on my
> github account :
>
>
>
> https://github.com/ggoret/MUDRA
>
>
>
> -          In /doc, I have placed a summary (a pdf slideshow) of the
> project containing some pictures (and info on instruments)
>
>
>
> -          In /examples I have put two data volumes (npy binary file
> format) the kind of data I need to register.
>
>
>
> -          In /mudra a first (naive) try using the Fourier shell
> correlation as metric
>
> And you can also find
>
> -          a Cython wrapping of malik and perona’s algorithms
> implementation working (pretty quickly) on 3D Volumes :
>
> o   /mudra/extensions/non_linear_filtering.pyx
>
>
>
> -          In /scripts you will find mainly converters simplifying I/O
>
> -          In /tools 3 very nice visualization tools based on VTK (not
> mayavi) working as standalone (npy input) :
>
> o   elevation.py -> 2d image to 3d landscape
>
> o   plan_interpolator.py -> 2d slicing of volume + isosurface rendering
> for given seeds
>
> o   scalar_field.py -> volume rendering (color and opacity gradient)
>
>
>
> Thanks in advance for your advices
>
>
>
> Cheers,
>
>
>
> Gael
>
>
>
> *De :* Neuroimaging [mailto:neuroimaging-bounces+gael.goret=
> cea.fr at python.org] *De la part de* Eleftherios Garyfallidis
> *Envoyé :* jeudi 20 août 2015 16:35
> *À :* Neuroimaging analysis in Python
> *Objet :* Re: [Neuroimaging] 3d registration for data fusion in material
> science
>
>
>
> Hi Gael,
>
>
>
> Sounds exciting. There is no restriction to use our tools in other
> libraries or domains.
>
> Look at these tutorials please (you need dipy development version)
>
>
>
>
> https://github.com/nipy/dipy/blob/master/doc/examples/affine_registration_3d.py
>
>
> https://github.com/nipy/dipy/blob/master/doc/examples/syn_registration_2d.py
>
>
> https://github.com/nipy/dipy/blob/master/doc/examples/syn_registration_3d.py
>
>
>
> Do you have a github repo of your project? Do you have any example
> pictures/volumes to show us that you would
>
> like to register?
>
>
>
> Cheers,
>
> Eleftherios
>
>
>
>
>
>
>
> On Thu, Aug 20, 2015 at 9:31 AM, GORET Gael 246279 <Gael.GORET at cea.fr>
> wrote:
>
> Hi everybody,
>
> I am a (French) newcomer, working on the development of the data fusion of
> Time-of-Flight Secondary Ion Mass Spectrometer (ToF-SIMS) and X ray
> Nano-Tomography (XuM) data at the CEA (the French state institute for
> energy, high-tech, etc.).
>
> In terms of samples, we’re a bit far from the neuro-fields … Solid oxide
> fuel cell, 3D chips, Si/Li matrix, etc., but in terms of methodology I hope
> we have to share … my project is to combine a chemical information (from
> ToF-SIMS) with X-ray absorption (given by XuM) for a given volume (at
> nano-scale).  I am tackling a python module aiming to the registration of
> 3d datasets. it seems that nipy includes a such possibility (an a lot more
> …).
>
> I’m a computer guy, mostly Pythonist and I wander if you would let  me
> transpose your code (mainly the registration part) to my problematic, I
> would be very grateful for this.
>
> In this context would you have some advice for me ?
>
> I'm looking forward to hearing from you.
>
> Gael
>
>
>
>
>
> *Dr. Gaël Goret*
>
> Chercheur Postdoctoral
>
> Département des Technologies Silicium
>
> *S*ervice de *C*aractérisation des *M*atériaux & *C*omposants
>
> Commissariat à l’énergie atomique et aux énergies alternatives
>
> MINATEC Campus *|* 17 rue des martyrs *|* F-38054 Grenoble Cedex
>
> T. +33 (0)4 38 7*8 49 29 **| *gael.goret at cea.fr
>
>
>
>
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-- 
Lead Clinical Research
Advanced Clinical Imaging Technology
Siemens/CHUV/EPFL
1015 Lausanne, Switzerland
Phone: +41 21 545 9972
https://sites.google.com/site/alexisroche
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