PyKar

Simple karyotyping tool in python/opencv

How to use:

Just call the script in python using image flag

$python main.py -i image_name

Notes

Problem description:

1. Resolving overlaps To separate overlapping chromosomes while retaining maximum resolution. Possible solutions:

    Solution A:
      Identify objects that are '+' or 'T' shaped
      Clone object
      Cut of corresponding arms
      (Maybe use houghlines?)
      
    Solution B:
      Allow user to select region
      Allow user copy and paste region
      Allow user to select and delete excess regions
      (Maybe be use grabcut OR build mini GUI in tk/qt)
      
    Solution C:
      Are other ways possible (?)
   

2. Feature extraction Identify chromsomes based on other characteristics when sizes are roughly similar.

    Identify banding pattern(?)
     How to recognize dark and light pixels of a foreground object?
    
   Identify centromere position (?)
     What makes centromere different from other regions of a chromosome in an image?
   

3. Visualizing Show all the chromosomes and allow user to rotate, switch and label/annotate according their analysis

     Possibly make a small interface with tk OR qt (Maybe there is a better alternative).