Noza23
commented
10 months ago @davetornado it is all yours
Closed Noza23 closed 10 months ago
Noza23
commented
10 months ago @davetornado it is all yours
Noza23
commented
10 months ago Moved to #13
[ ] Area of Myotubes - Area of instances [µm2]
[ ] Area of Nuclei - Area of instances [µm2]
[ ] Number of Myotubes - Number of myotube instances
[ ] Number of Total Nuclei - Number of all nuclei instances
[ ] Number of Myoblasts - Nuclei instances outside of myotube instances (95% of nucleus area must be outside of an instance)
[ ] Number of Nuclei in Myotubes - Nuclei instances inside of myotube instances (95% of nucleus area must be inside of an instance)
[ ] Number of Nucleis Cluster - nuclei area must overlap minimum 10%
[ ] Nucleis per Nuclei Cluster - Number of Nuclei in each Nuclei Cluster
[ ] Total Fusion Index - Number of Nuclei in Myotubes / Number of Total Nuclei
[ ] Instance Fusion Index - Number of Nuclei per Myotube Instance
[ ] Centroid - The center point of the myotube instance. This is the average of the x and y coordinates of all of the pixels in the image or selection.
[ ] Perimeter - The length of the outside boundary of the instance.
[ ] Fit Ellipse - Fit an ellipse to the instance. Uses the headings Major, Minor and Angle. Major and Minor are the primary and seconday axis of the best fitting ellipse. Angle (0-180 degrees) is the angle between the primary axis and a line parallel to the x-axis of the image. The coordinates of the center of the ellipse are displayed as X and Y if Centroid is checked.
[ ] Circularity - 4π*area/perimeter^2. A value of 1.0 indicates a perfect circle. As the value approaches 0.0, it indicates an increasingly elongated shape. Values may not be valid for very small particles.
[ ] Aspect ratio - major_axis/minor_axis.
[ ] Roundness - 4area/(πmajor_axis^2), or the inverse of the aspect ratio.
[ ] Solidity - area/convex area (maybe scipy.spatial.ConvexHull)
[ ] Feret's Diameter - The longest distance between any two points along the selection boundary, also known as maximum caliper (https://github.com/matthiasnwt/feret)
[ ] Mean Gray Value per Myotube - Average gray value within the myotube instance for each channel (RGB or even more for TIF stacks).
[ ] Gray Value Standard Deviation per Myotube - Standard deviation of the gray values for each channel per myotube instance.
[ ] Modal Gray Value per Myotube - Most frequently occurring gray value for each channel within the myotube instance.
[ ] Median Gray Value per Myotube - The median gray value of the pixels and chanel in the myotube instance.
[ ] Min & Max Gray Level Median Gray Value per Myotube - Minimum and maximum gray values for each channel within a myotube instance.
[ ] Integrated Density - the product of Area and Mean Gray Value