Wandell Lab

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'''Welcome to the VISTA LAB Wiki! '''
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These web pages describes the Magnetic Resonance Imaging and Image Systems Engineering activities in the Wandell lab.
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This manual describes the [[Software|software]], experimental methods and administrative procedures used in the Wandell lab. Manual pages that describe the software and analytical methods are organized into major manual sections by the menu at the left.  
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We perform our MRI measurements at  [http://cni.stanford.edu/ Stanford's Center for Cognitive and Neurobiological Imaging] (CNI).  
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Description of the MR scanner and protocols we are using can be found in [http://cni.stanford.edu/wiki wiki pages] Stanford's Center for Cognitive and Neurobiological Imaging (CNI).  
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We work on Image Systems Engineering through the support of [http://scien.stanford.edu Stanford's Center for Image Systems Engineering] (SCIEN).
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=== MR Software  ===
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= MRI Research =
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== MR Software  ==
For the last decade we have shared software from our lab freely. An overview of all the software, and links to software and test data downloads, are in [[Software]]. There are large wiki sections describing distinct software components for  
For the last decade we have shared software from our lab freely. An overview of all the software, and links to software and test data downloads, are in [[Software]]. There are large wiki sections describing distinct software components for  
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General purpose software
*[[Anatomical Methods|Anatomical methods]]  
*[[Anatomical Methods|Anatomical methods]]  
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*[[Stimulus|Stimulus generation ]]
*[[Stimulus|Stimulus generation ]]
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=== MR Analysis methods ===
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Specific methods
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These pages also describe the methods we have developed within these packages.
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*[[Retinotopy Tutorial|Visual field map measurement]]  
*[[Retinotopy Tutorial|Visual field map measurement]]  
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*[[ConTrack|Fiber Tracking]]  
*[[ConTrack|Fiber Tracking]]  
*[[Tensor Statistics]]  
*[[Tensor Statistics]]  
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*[[NIMS User Example|Neurobiological Image Management System]]
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*[[AFQ | Automated Fiber Quantification]]
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*[[LiFE | Linear Fascicle Evaluation]]
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=== Vision modeling methods  ===
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To add (pointers to the work with Aviv, Franco, Hiromasa and Ariel): qMRI, ET
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*[[VSET|Visual system engineering tool]]
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== Reproducible Research ==
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=== Local interest ===
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*[http://post.stanford.edu Project on Scientific Transparency]
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*[http://flywheel.io Flywheel: A commercial venture to support reproducible research]
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*Manual pages specific to our Stanford laboratories, and not of general interest, are [[Administrative]], and [[Vision Lunch]].
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== Local interest ==
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*A place for [[White papers|lab white papers and historical notes of interest]].
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*Manual pages specific to our lab, and not of general interest, are [[Administrative]], and [[Vision Lunch]].
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*[[Scanning Instructions]] for the Lucas center scanners (password-protected).
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*[[White papers|lab white papers and historical notes of interest]]
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*[[CNI Scanning Instructions]] (password-protected).  
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*In-progress [[Local projects]]
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*[[Sun Grid Engine]]  
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*[[Computer list]]
*[[Computer list]]
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This wiki describes software and experimental methods developed for digital imaging applications in the [http://vistalab.stanford.edu VistaLab]. The work here is done in collaboration with members of [http://scien.stanford.edu Stanford's Center for Image Systems Engineering].
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= Image Systems Engineering Research =
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There is a [[Software|PDC Software]] page that explains how to download software and use SVN.  
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The work here is done in collaboration with members of [http://scien.stanford.edu Stanford's Center for Image Systems Engineering] (SCIEN).
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If you are a new lab member and would like to review general issues please visit the [http://white.stanford.edu/newlm/index.php/Administrative#New_lab_member Vistalab new member page]
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== Jupyter calculations ==
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=== Current PDC projects ===
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Many of the Image Systems Simulation calculations are performed using either ISET or ISETBIO.  You can run some demonstration scripts with this software at our [[ISETBIO Jupyter]] hub site.  
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*[[L3 Algorithm]] - Local, linear learned - Automatic image process pipeline learning for arbitrary CFAs
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== Current projects  ==
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*[[ISET-Depth|Scene 3D (Andy Lin)]]
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*[[Colorblind Metric|Metric, Simulations, Experiments for Colorblind]]
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*[https://github.com/isetbio/isetbio ISET for biology]
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=== Previous and Related PDC projects  ===
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*[[L3 Algorithm (Haomiao Jiang, Qiyuan Tian]] - Local, linear learned - Automatic image process pipeline learning for arbitrary CFAs
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*[[ISET-Depth|Scene 3D and CISET (Andy Lin, Trisha Lian)]]
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*[[Colorblind Metric|Metric, Simulations, Experiments for Colorblind (Haomiao Jiang)]]<br>
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*[http://computational-eye-brain.org Computational Eye Brain], [https://github.com/isetbio/isetbio Image systems engineering toolbox for biology], [https://github.com/isetbio/isetbio/wiki ISETBIO wiki page]
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== Related SCIEN projects  ==
*[[ISET]]  
*[[ISET]]  
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*[[Reflectance and Illuminant Estimation]] - New ideas about these old problems
*[[Reflectance and Illuminant Estimation]] - New ideas about these old problems
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=== '''Image databases and related''' ===
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== Image databases and related  ==
*[http://scarlet.stanford.edu/validation Local Data Sets]
*[http://scarlet.stanford.edu/validation Local Data Sets]
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*[http://www-isl.stanford.edu/~abbas/group/imaging.shtml Programmable digital camera (PDC) project]
*[http://www-isl.stanford.edu/~abbas/group/imaging.shtml Programmable digital camera (PDC) project]
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=== '''Contributors'''  ===
 
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Haomiao Jiang, Qiyuan Tian, Henryk Blasinski, Manu Parmar, [http://scien.stanford.edu/jfsite/index.html Joyce Farrell], Steven Lansel, Jiajing Xu, [http://www.stanford.edu/~pcatryss Peter Catrysse] and [http://vistalab.stanford.edu/wandell.html Brian Wandell]. You may be interested to browse through [http://scien.stanford.edu/class/psych221/projects/ a large collection of student projects related to this work].
 

Latest revision as of 16:47, 11 January 2016

These web pages describes the Magnetic Resonance Imaging and Image Systems Engineering activities in the Wandell lab.

We perform our MRI measurements at Stanford's Center for Cognitive and Neurobiological Imaging (CNI).

We work on Image Systems Engineering through the support of Stanford's Center for Image Systems Engineering (SCIEN).

Contents

[edit] MRI Research

[edit] MR Software

For the last decade we have shared software from our lab freely. An overview of all the software, and links to software and test data downloads, are in Software. There are large wiki sections describing distinct software components for

General purpose software

Specific methods

To add (pointers to the work with Aviv, Franco, Hiromasa and Ariel): qMRI, ET

[edit] Reproducible Research

[edit] Local interest

[edit] Image Systems Engineering Research

The work here is done in collaboration with members of Stanford's Center for Image Systems Engineering (SCIEN).

[edit] Jupyter calculations

Many of the Image Systems Simulation calculations are performed using either ISET or ISETBIO. You can run some demonstration scripts with this software at our ISETBIO Jupyter hub site.

[edit] Current projects

[edit] Related SCIEN projects

[edit] Image databases and related

Curated list of image databases

Image databases

Hyperspectral databases

Deprecated

Personal tools