Segmentation

One of SPARTANs main purposes is to extract and analyze particle datasets. This feature will extract individual particles from an SMLM dataset using a corresponding single widefield snapshot as a guide for the segmentation.

Select Particle Segmentation from the SPARTAN menu.\

1. Select the type of dataset, i.e. single- or dual-color and load the corresponding wide field and localization datasets. Important: To allow easy batch processing, you can load the file information from a generated input file. An example input file can be found in the example data folder.
2. Select the type of segmentation
   • OTSU segmentation (using the function greythresh)is typically used for very bright and isolated particles.
   • The manual segmenter option allows to adjust the thresholds manually, which can help to segment low contrast particles. Important: We suggest to try both segmenter options, typically using the higher contrast WF image.

3. Perform the segmentation
4. Extract particles from the dataset. Here we advice to select a minimum number of localizations for both channels in order to keep only double-labelled particles.

5. Save the particles.