Journal: Scientific Reports

Article Title: RHYTHM: An Open Source Imaging Toolkit for Cardiac Panoramic Optical Mapping

doi: 10.1038/s41598-018-21333-w

Figure Lengend Snippet: Calibration of geometry and optical cameras. ( A ) A MATLAB graphical user interface was used to semi-automate the calibration of each camera needed to facilitate the projection of optical data onto the geometric surface. Detailed explanations and code are included in the toolkit. ( B ) The cuboid is used to create a global coordinate system whose origin is at the cuboid’s center. All grid junctions on the cuboid surface have known coordinates in the global coordinate system. Identification of these points in a 2D image provides the necessary number of known values to solve for the unknown components of the global-to-camera (i.e., transformation) and the camera-to-sensor (i.e., perspective projection) matrices.

Article Snippet: We then uploaded these images to our custom written MATLAB GUI (Fig. ) that facilitates the identification of the heart silhouette in each image using a combination of thresholding and polyline tools.

Techniques: Transformation Assay

Journal: Scientific Reports

Article Title: RHYTHM: An Open Source Imaging Toolkit for Cardiac Panoramic Optical Mapping

doi: 10.1038/s41598-018-21333-w

Figure Lengend Snippet: Geometric reconstruction. ( A ) A MATLAB graphical user interface was developed to facilitate accurate identification of the heart silhouettes needed for geometric reconstruction. A detailed description and the code are included in the toolkit. ( B ) The heart was rotated, and binary silhouette images were collected every 5 degrees. ( C ) Using the occluding contours method paired with an octree algorithm a series of voxels are iteratively broken down to identify the heart volume. ( D ) The surface mesh is generated by MATLAB from this volume and smoothed by external C function.

Article Snippet: We then uploaded these images to our custom written MATLAB GUI (Fig. ) that facilitates the identification of the heart silhouette in each image using a combination of thresholding and polyline tools.

Techniques: Generated

Journal: Scientific Reports

Article Title: RHYTHM: An Open Source Imaging Toolkit for Cardiac Panoramic Optical Mapping

doi: 10.1038/s41598-018-21333-w

Figure Lengend Snippet: Data processing and projection ( A ) A final MATLAB graphical user interface was created to facilitate the processing of optical data and its projection onto the representative geometry. ( B ) Projection is accomplished by projecting the face centroids of the triangulated mesh onto the optical mapping cameras. Tools are provided to correct minor inaccuracies in projection. Camera facing centroids are first identified as those whose normals ( N cell ) creates an angle greater than 90° with the camera normal ( N ic ). ( C ) The surface can then be visualized as a triangulated mesh (i), a map of the camera assignments made to each centroid (ii), texture (iii), and membrane potential (iv). ( D ) Once correspondence has been established the geometry will appear with membrane potential mapped to the surface. Tools are provided to rotate the heart using click-and-drag, to the view from each camera, and to specific viewing angles using azimuth and elevation angles.

Article Snippet: We then uploaded these images to our custom written MATLAB GUI (Fig. ) that facilitates the identification of the heart silhouette in each image using a combination of thresholding and polyline tools.

Techniques: Membrane