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Temporal Superresolution

Introduction

One of the biggest challenges in fluorescence microscopy is imaging with a low photon count. This often leads to images and movies with a low signal to noise ratio (SNR). One way to improve SNR is to increase the integration (exposure) time, thus collecting more photons per image. However, this results in a loss of temporal resolution, which can be problematic when imaging fast, dynamic processes (such as the beating heart). Our temporal superresolution approach improves both SNR and temporal resolution by combining multiple 2D+time cycles of a repeating process into one ideal, denoised, high-speed movie. We present the algorithm as a FIJI plugin that can be applied to any 2D+time movie containing multiple repeating cycles.


To download the plugin, click here.


Installation

1. Download FIJI (if you don't already have it) and our plugin.

2. Unzip the plugin.

3. Copy the Temporal Superresolution folder into the Fiji/plugins folder.

4. Our plugin also relies on an external library, JTransforms 3.1. Download the JTransforms library (JTransforms-3.1-with-dependencies.jar) from https://sites.google.com/site/piotrwendykier/software/jtransforms and place the JTransforms-3.1-with-dependencies.jar file in the Fiji/jars folder.


Example Usage

1. Start Fiji, and load a multicycle 2D + time dataset. Select "Temporal Superresolution" from the Plugins menu.

Running the temporal superresolution plugin in Fiji.

2. You will be prompted to confirm the image stack you wish to process.

Running the temporal superresolution plugin in Fiji.

3. You will be prompted to select a region of interest to be used for temporal registration. You may wish to use the rectangle tool for ROI selection, or you may proceed without selecting a region of interest, in which case the entire image will be used. After clicking "OK", the plugin will proceed with its initial temporal registration, which may take a few seconds depending on the number of timepoints in your data.

Selecting a region of interest.

4. After temporal registration, the plugin will provide an estimate for the number of frames in one cycle of your repeating process. It will also ask you for your desired frame-rate gain factor (recommended = 2), and it will provide an estimate of the optimal value of the regularization parameter. You may use these estimated values, or you may input custom values. Also, by default, the "Fast Approximation" box is unchecked. Clicking "OK" with the "Fast Approximation" box unchecked solves the algorithm using the \(\ell_1\) norm. You may check this box to solve using the \(\ell_2\) norm (faster, but worse quality).

5. After processing, the plugin will display the reconstructed cycle with improved signal-to-noise ratio and improved temporal resolution in a separate image window.

Temporal superresolution output.

References

[1] K. G. Chan, S. J. Streichan, L. A. Trinh and M. Liebling, "Simultaneous Temporal Superresolution and Denoising for Cardiac Fluorescence Microscopy," in IEEE Transactions on Computational Imaging, vol. 2, no. 3, pp. 348-358, Sept. 2016.

[2] K. Chan, L. A. Trinh, M. Liebling, "A temporal superresolution method applied to low-light cardiac fluorescence microscopy", Asilomar Conference on Signals, Systems and Computers, 2013.

Download

Modified BSD-2 License - for Non-Commercial Research and Educational Use Only

Copyright (c) 2016, The Regents of the University of California


All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted for non-commercial research and educational use only provided that the following conditions are met:


1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.


THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
For permission to use for commercial purposes, please contact UCSB's Office of Technology & Industry Alliances at 805-893-5180 or info@tia.ucsb.edu.

Download plugin: Download plugin

Download sample data: Zebrafish Heart Data