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

Fri Aug 21 15:07:44 CEST 2015

Yes, nireg can recover an anisotropic scaling using a 12-parameter affine
transform (this would also estimate a shearing effect) or an isotropic
scaling using a similarity transform (7 parameters).

Alexis
Le 21 août 2015 12:54, "GORET Gael 246279" <Gael.GORET at cea.fr> a écrit :

> The nireg repo was originally which push me to contact the Neuroimaging
> group.
>
> Apart some scaling issue (anisotropic pixel spacing), the rigid body
> approach should suit to my problematic.
>
>
>
> The following snippet :
>
> https://github.com/nipy/nireg/blob/master/examples/affine_registration.py
>
> seems a good starting points to me.
>
>
>
> The magic is confine  into the HistogramRegistration class in the
> following module :
>
>
> https://github.com/nipy/nipy/blob/master/nipy/algorithms/registration/histogram_registration.py
>
> The code seems tricky, but with a lot of comments and docstrings !! it
> could have been  much much worse :)
>
>
>
> Questions :
>
> -          how to convert a numpy array to nipy-like image ?
>
> -          should the two images have the same size ?
>
> -          the version of nipy that I should use ?
>
>
>
>
>
> thank you, really, for your attention, this is kind.
>
>
>
> Gael
>
>
>
>
>
>
>
>
>
> *De :* Neuroimaging [mailto:neuroimaging-bounces+gael.goret=cea.fr at py
> thon.org] *De la part de* Alexis Roche
> *Envoyé :* vendredi 21 août 2015 13:04
> *À :* Neuroimaging analysis in Python
> *Objet :* Re: [Neuroimaging] 3d registration for data fusion in material
> science
>
>
>
> 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
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