# MUSIC: Cardiac Imaging, Modelling and Visualisation Software for Diagnosis and Therapy
## 4 Functionalities
### Segmentation  
The Segmentation workspace handles multiple segmentation tools, one of the most important and used is the \"Polygon ROI\" toolbox. The \"Polygon ROI\" toolbox has been developed jointly by our team and radiologists. This tool allows us to manually segment images through polygon contours (ROI, region of interest), use a repulsor tool to refine these contours, automatically interpolate these segmentations between slices, or annotate them for AI. A focus in the development has been made on the production of contours with standardised labels. For now, eight different structures with different colours and names can be defined simultaneously. Figure 5 illustrates the ability to segment several anatomical zones and define a label name for each structure.  
Figure 5: Contours segmented in polygon ROI toolbox. This example shows an ongoing segmentation of the left (green) and right (blue) ventricles of the heart.  
\begin{table}
\begin{tabular}{p{85.4 pt} p{284.5 pt}} \hline \hline
**Worspace** & **Description** \\ \hline Diffusion & Processing of diffusion and tractography. \\ \hline EAM Analysis & Electroanatomical mapping analysis tools. \\ \hline Filtering & Image binary operation (AND, OR, XOR, NOT), constant operation (addition, multiply, etc.), blurring, normalisation, thresholding, edge filters, mask application, morphological filters (dilate, erode, close, open), bias correction, etc. \\ \hline Meshing & Convert mesh to and from mask, data array management, interpolation, projections, distance computations, mesh deformation, morphological mesh filters, binary operations on meshes, fiber computations, decimation, refine, etc. \\ \hline Reformat & Crop data, extract 3D data from 4D ones, merge images and meshes, reslice (change orientation, pixel size, image dimensions), super resolution (compute accurate data from orthogonal ones), move an image to a new location. \\ \hline Registration & Register two images with diffeomorphic demons [6], LCC Log demons, Optimus registration algorithm (gradient-free Mutual Information-based rigid registration), or manual registration. \\ \hline Radiotherapy & Radiotherapy ablation planning tools with DICOM-RT-STRUCT data. \\ \hline Segmentation & Mapping of myocardial depth isthmuses, histogram analysis, level set segmentation, paint and polygon segmentations, VOI (volume of interest) segmentation, variational segmentation through landmarks, as well as vessel segmentation. \\ \hline Simulation & Simulation processing tools, forward problem, inverse problem, FEM and MFS simulation tools (see Section 4.5). \\ \hline \hline \end{tabular}
\end{table}
Table 3: List of the main imaging and meshing tools in MUSICradio.  
The results of segmentation can be saved as binary masks or internal contours structures. A contour structure is an internal format of MUSICardio and medInria. It allows us to save the work in progress and start again later or reuse the result of a segmentation as the model on another dataset. Other useful features are available:  
* Correction tools: each node of the polygon contour can be manipulated separately, or a repulsor tool is available allowing to push the segmentation boundary with a circle. See Figure 6a.
* Multiple Views: segmentations can be done on different series simultaneously in multiple views to keep the same label name for series, and we can use a cursor to mark a position in series. The data have to be first reformatted. Figure 6b shows two MRIs at different dates. A lesion, in green, is visible only on one series (the right one). The evolution of another lesion is showed on the second series in blue. The green cursor allows us to find the way through the images.