Abstract
We present an algorithm, and its MATLAB implementation, based on mathematical methods to detect and localize 3D multicolor DNA FISH spots in fluorescence cell image z-stacks. This algorithm provides a method to measure the relative positioning of spots in the nucleus and inter-spot distances with the aim to enrich our understanding of the 3D spatial organization of the genome within the cell nucleus.
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Notes
- 1.
The pixels labeled 0 are the background. The pixels labeled 1 make up one object; the pixels labeled 2 make up a second object; and so on.
- 2.
Pixels are connected if their edges or corners touch.
- 3.
Pixels are connected if their faces touch.
- 4.
Pixels are connected if their faces, edges, or corners touch.
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Gregoretti, F., Cortesi, A., Oliva, G., Bodega, B., Antonelli, L. (2021). An Algorithm for the Analysis of the 3D Spatial Organization of the Genome. In: Bodega, B., Lanzuolo, C. (eds) Capturing Chromosome Conformation. Methods in Molecular Biology, vol 2157. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0664-3_17
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DOI: https://doi.org/10.1007/978-1-0716-0664-3_17
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