Dataset Title:
Data from: In Vivo Calcium Imaging of Cardiomyocytes in the Beating Mouse Heart with Multiphoton Microscopy

Zipped files in dataset:
Jones_Small_Nishimura_ FrontPhysiol_2018_ImageStacks
Jones_Small_Nishimura_ FrontPhysiol_2018_MatlabCode

Dataset Description:  
One zipped folder contains two-photon microscopy, in vivo images from the ventricle of a mouse expressing GCaMP6f in cardiomyocytes in three tif stacks. Ch1 pixel values are proportional to ventilator pressure. Ch2 pixel values are proportional to ECG voltage. Ch3 pixel values are fluorescence intensity values in the GCaMP channel. 

Data acquisition parameters: 50 frames per z slice
2 micrometers axial sampling 512x512 pixels in x and y 31.25 fps 
Images span a 24-micrometer deep imaging volume.For more details, please refer to: JS Jones, DM Small, and N Nishimura. "In Vivo Calcium Imaging of Cardiomyocytes in the Beating Mouse Heart with Multiphoton Microscopy" Frontiers in Physiology, 2018.

The other zipped folder contains the Matlab code used to sort multiphoton microscopy image data with simultaneously recorded ECG and ventilator pressure data by phase in the cardiac and respiratory cycle and position. 

This code was developed using Matlab version 2017a.
1. Unzip file and put contents of folder on Matlab path.  
2. Current directory should contain 3 separate image files labeled Ch1-filename.tif (respiration trace), Ch2-filename.tif (ECG trace), and Ch3-filename.tif (fluorescent channel being analyzed, as further outlined in the comments 
3. Run the function cardioresp_reconstruction with input parameters as outline in the comments an example of function call is 
[Lookuptable, QRSdata, Respiratorydata,x_B,x_r,Reconstion,SliceLevel] = cardioresp_reconstruction(50,2,10,15,'cardiac’,25,50,32,512,’Mouse1’);
4.  A sample GCaMP data set is included that has 50 frames per z slice, 2-um axial sampling, and 512x512 pixels. that is taken through a 24-um imaging volume. 

Licensing information:
These data are shared under two different licenses.
Images are shared under a Creative Commons Attribution 4.0 International license (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/), and may be openly used, shared and adapted, but appropriate attribution to the authors must be given (see citation information below).

Code is shared under a BSD-3 license. Copyright 2018 Jason Scott Jones, David Machin Small and Nozomi Nishimura. Redistribution and use in source and binary forms, with or without modification, are permitted 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. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 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.

Please cite this dataset as: 
JS Jones, DM Small, and N Nishimura. 2018. Data from: In Vivo Calcium Imaging of Cardiomyocytes in the Beating Mouse Heart with Multiphoton Microscopy. eCommons Digital Repository.  https://doi.org/10.7298/X41N7Z9D

Please cite the related publication as:
JS Jones, DM Small, and N Nishimura. "In Vivo Calcium Imaging of Cardiomyocytes in the Beating Mouse Heart with Multiphoton Microscopy" Frontiers in Physiology, 2018. doi: 10.3389/fphys.2018.00969.  

Contact:
Nozomi Nishimura
nn62@cornell.edu