Hosuk:LabNotes/2013-10-24
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Rolony count with PISA
1 tile, 2048 x 2048 image
- Sample : Confocal image of S2 MatTek dish at 2013-10-22
- Cells : about 70 cells, counted cells just by eye based on compact rolonies (assume nucleus)
- 1st Rolony (Cy5) parameters
- Area Upper : 100 px, Area lower : 2 px,
- Axioratio lower 0.7, Circ Upper 1.6 Circ Lower 0.4
- Perim conn 8, bkgmulti lower 2
- Count --> 5210 (about 74.4 cells per cell)
- ACTB (ATTO488) parameters
- Area Upper : 100 px, Area lower : 2 px,
- Axioratio lower 0.7, Circ Upper 1.6, Circ Lower 0.4
- Perim conn 8, bkgmulti lower 2
- Count --> 69 (about 1 cells per cell)
- Overlapped ACTB --> 40 (about 0.57 cells per cell)
- Overlapped ACTB / 1st rolony = 40/5210 = 0.77%
- Overlaped with ATTO488 on Cy5
- Blue : Cy5, Red : ATTO488 : Raw
File:ATTO488SegOverlapwithCy5 S2 20131022.png
Multiple 7 x 6 tiles, --> 11334 x 13077 image
- too big to process...
Multiple 7 x 6 tiles, --> Cropped to 4 x 4 --> 7453 x 7453 image
- Try...