5 Puncta Extraction

The puncta extraction stage attempts to find puncta in the registered images. All rounds are combined into a basename_allSummedNorm file created in the puncta extraction directory. Puncta are attempted to be found in this combined image with a combination of thresholding to remove background and watershed to find potential puncta regions. These candidate regions are judged to be puncta based on the parameters:

• params.PUNCAT_SIZE_THRESHOLD
• params.PUNCTA_SIZE_MAX

An image visually showing the found puncta is created in a file marked basename_allSummedNorm_puncta.

Two .mat files are also created:

• basename_centroids+pixels
• basename_punctavoxels

The basename_centroids+pixels.mat contains a puncta_centroids matrix with a row per puncta containing the X,Y,Z co-ordinates of the found puncta. The .mat file also contains a puncta_voxels cell array per puncta describing the shape of the found puncta.

The basename_punctavoxels.mat contains two variables puncta_set_cell and puncta_indices which contain additional information for each of the found puncta.