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Nucleus Classification

Nucleus Classification. By Venkata sandeep kumar Chithirala Harik kumar Mahareddy Harsha Gaddam. Objectives. Classification of nuclei. Based on circularity , volume , density/texture. Volume ,area and density of nucleolus.

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Nucleus Classification

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  1. Nucleus Classification By VenkatasandeepkumarChithirala HarikkumarMahareddy HarshaGaddam

  2. Objectives • Classification of nuclei. • Based on circularity , volume , density/texture. • Volume ,area and density of nucleolus. • Volume ,area and density of heterochromatin.

  3. Actual nucleus

  4. Nucleus given in the 3DEM DATA

  5. Features • The nucleolus is not constant it keeps on changing from one slice to other slice. • The nucleus position is also not constant . • Some particles look similar to nucleus.

  6. Plugin • Automatic segmentation and finding the position of various nucleus. • Using filters and threshold. • Then we take those positions and select regions in original image and then calculate the various aspects required . • Particular nucleus present at a position is considered and then we move through all slices to get the best output.

  7. Automatic selection of the nucleus • Firstly we apply bilateral filter . • Then we apply the sobel edge detection. • By adjusting the threshold values and analyzing the particles we find the nucleus positions. • Then we find the maxima so that we get the seed points. • The above process is done by a single click of the custom plugin we developed.

  8. Result of segmented image with seed points

  9. Volume Calculation • By taking the seed points we calculate the values of the volume. • Each particle is given a label and area is calculated in each slice and all areas are calculated for the same label and volume is calculated. • We fit the best ellipsoid into the segmented objects and find the radius . And display min and max radius.

  10. Result

  11. Results Table

  12. Code snippets

  13. Code snippet

  14. Future work • Working on density and texture calculation. • And to develop a final plugin where no user input is required and all the process is automated.

  15. References • http://rsbweb.nih.gov/ij/download.html • http://www.youtube.com/watch?v=8c68qIz_ftw • http://www.youtube.com/watch?v=8U_OGk1XObE • http://www.biomedcentral.com/1471-2121/8/40 • https://github.com/mdoube/BoneJ/tree/master/src/org (used for calculation of volume)

  16. Thank you

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