Lightfieldscope.org

Lightfield microscopy for high-speed, three-dimensional,

simultaneous imaging of neural dynamics



Explore
Read the papers, etc.
Hardware
DIY / Build it yourself
Software
Download code and executables
 
 
 

Welcome to our site for learning how to build and use lightfield neural activity imaging microscopes, which enable simultaneous, high-speed, three-dimensional imaging of neural activity.

Here you can find relevant papers, hardware descriptions, parts lists, manuals, software, and advice on lightfield neural activity imaging.

This is a joint production between


Contact Information

Please send inquiries to info@lightfieldscope.org


References and Links

Prevedel*, Yoon*, et al. (2014) Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy, Nature Methods 11:727730. [Publisher link]

Other relevant references:
Levoy et al., ACM Trans. Graph, 2006 [Publisher link] - First paper describing light-field microscopy, 2006
Broxton et al., Optics Express, 2013 [Publisher link] - An improved algorithm for light-field microscopy, 2013

News

[Video reveals entire organism's neurons at work (Nature, 5/18/2014)]
[High-speed imaging method captures entire brain activity (IMP, 5/19/2014)]
[Illuminating neuron activity in 3-D (MIT News, 5/18/2014)]
[Neurons in Action (The Scientist, 5/19/2014)]
[Neuronal Imaging System Shows Bigger 3-D Picture (Photonics.com, 5/19/2014)]
[Engineers ask the brain to say, "Cheese!" (NSF, 5/19/2014)]
[Scientists Visualize Entire Nervous System of Worm in Real-Time 3D (PBS/NOVA, 5/20/2014)]
[Worm's Entire Nervous System Captured Firing In Real Time (Huffington Post, 5/20/2014)]
[High-speed imaging method captures entire brain activity (Optics.org, 5/22/2014)]

Gallery


Freely moving C. elegans:

Zebrafish:

Commercial Partners

Developing.

Hardware


The resources for building LFM hardware are available below.


Version 1.0

This is a tutorial for building a LFM with emphasis on alignment for high quality reconstruction.



Build Your Own

An LFM system appended to an epifluorescence microscope is shown below. For more detailed explanation of parts and assembly, please refer to the PDF tutorial above.

Photograph

View from front of scope body:



View from side of scope body:

Software


The software for 3D volume reconstruction from light-field images is available below.


Version 1.0

This is the code originally used in the Nature Methods, 2014, paper. It is written in MATLAB and requires a workstation with MATLAB2013a or later version and at least 32GB of RAM. The manual, in PDF format, describes how to use the code.