Algorithm 5: Single Particle Detection and Picking

1. Input: $I_{cs}$ /* cleaned cluster image with square shapes only */

2. Return: $I_{cps}$ /* cleaned cluster image with perfect square shapes */

3. $\mathrm{L}\leftarrow \mathrm{bwlabel}\left({\mathrm{I}}_{\mathrm{c}1}\right)$ /* label each object in the cluster image */

4. for i = 1 to $L$ do /* for each object in the clustered image */

5.  $\mathrm{Stats}\leftarrow \mathrm{regionprops}\left({\mathrm{I}}_{\mathrm{cs}}\right)$/* measure properties of particle region */

6.   Areas ← [props.Area /* compute all the shape measurements and the pixel value measurements as well */

7. end for

8. for $i$ = 1 to $size\left(keeperObjects\right)$ do/* for each particle object */

9.  $\left[x,y\right]\leftarrow centroid\left(keeperObjects\right)$/* extract the centroid is the horizontal coordinate (or x-coordinate) and vertical coordinate (or y-coordinate) */

10.  Draw all bounding box for a discontinuous region

11. end for