Difference between revisions of "Spring 2012:LFM Report"
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# Frank Warmerdam, Andrey Kiselev, Bob Friesenhahn, Joris Van Damme and Lee Howard for raw2tiff tools. | # Frank Warmerdam, Andrey Kiselev, Bob Friesenhahn, Joris Van Damme and Lee Howard for raw2tiff tools. | ||
+ | == References == | ||
<references/> | <references/> | ||
{{Template:20.345 bottom}} | {{Template:20.345 bottom}} |
Revision as of 07:31, 17 May 2012
Contents
Light Field Microscope
Vincent Lee & Leanna Morinishi
Introduction
Background and Motivation
Traditional light microscopy has been used to illuminate miniature biological specimens since the mid-1600s. Since, researchers have come to realize and (attempt to) circumvent the inherent limitations of the technique. One such limitation is that of superimposed features on the captured image. With no depth information from the subject, it is difficult to extract data specific to the focal plane from the rest of the image.
Confocal microscopy excludes light from above or below the focal plane of the image using a pinhole placed where the light from the focal plane comes to a waist. It also provides a method of visualizing 3-dimensional images and has better spatial resolution than light field microscopy, but images require scanning the entire sample at every depth of interest. Light field has the advantage of capturing relative depth information in a single photo. This additional visual information comes at a cost, however. Diffraction places an upper limit on the lateral and axial resolution of the images. We thus sacrifice spatial resolution to obtain angular resolution.
The light field microscope allows angular resolution information to be recorded in a single image. The light field is a function that represents the amount of light traveling in every direction through every point in space. By recording a sample’s light field, one can produce perspective and parallax views of the specimen. This is accomplished by inserting a microlens array in a conventional bright field microscope, and analyzing the images in silico. A microlens array is an optical component containing a spread of thousands of lenses with diameters in the micron scale. Applying 3D deconvolution to the focal stacks from the array produces a series of cross sections which allow for a 3D reconstruction of the sample.
The objective of this project is to create a light field microscope from a Lytro™ camera and the Thorlabs materials available in the 20.345 classroom, record associated documentation and code, and describe recommended experiments for use in a teaching undergraduate laboratory.
Prior Work
The only prior work we have to build upon are papers by Ren Ng's original paper on the light field microscope[1], his further work[2], his thesis[3], and some great work from a postdoc at Harvard[4]. This project has not been done previously in the 20.345 lab.
Design
Optical Setup
The microscope design went through a few iterations and continues to evolve. We originally tried to use a 2" lens telescope to magnify the image. At first the telescope was before the tube lens, but since that contributes to aberration it was placed after the tube lens. While doing this, we realized that the image should be in focus just before the Lytro™ optics.
We tried to put a different tube lens in the system to magnify the image with a single lens, however the led to a considerable amount of spherical aberration.
Image Processing
Reverse engineering the Lytro™ images
Creating .jpg image stacks from -stk.lfp
Creating .raw from .lfp
Creating .tif from .raw
Dealing with the hexagonal microarray
List of parts
Methodology
Disassembling the Lytro
Aligning the beam path
Making sample slides of fluorescent beads
Acknowledgments
- Nirav Patel, for reverse engineering the Lytro image and lfpsplitter.
- Frank Warmerdam, Andrey Kiselev, Bob Friesenhahn, Joris Van Damme and Lee Howard for raw2tiff tools.