AT PK - Automatic particle picking - peak search

PURPOSE

Peak search over a specific region corresponding to the dimensions of the particle. Only peaks over the specified threshold are retained. Picks positive peaks only (bright particles on dark background). Depending on the window dimensions peaks close to the edge of the micrograph are excluded.

SEE ALSO

AT WN	[Automatic particle selection]
AT SA	[Automatic particle picking - statistical parameters ||]
AT IT	[Automatic particle picking - intermediate program.]

USAGE

.OPERATION: AT PK

.INPUT FILE: FIL001
[Enter name of filtered image for peak search.]

.NEIGHBORHOODPOINTS PIXELS FOR SEARCH: 13
[Enter the number of pixels which corresponds approximately to the size of the particle. The filtered image is searched for peaks over a region equal to 13 pixels in this case i.e., the highest peak in a 13 by 13 square is considered. This way picking up the same particle is avoided and also nearest neighbour distance is taken into account. Must be 3 or greater.]

.THRESHOLD FOR PEAKS: 0.7
[Enter the threshold value i.e., only peaks having correlation coefficients over this value are picked up.]

.MICROGRAPH EDGE DIMENSIONS: 80,80
[Peaks closer to the edge of the micrograph are excluded. i.e.,in the example if x1and y1 are the x- and y- corrdinates of the peaks, and ns,nr,nsam and nrow are the dimensions of the micrograph edge and the micrograph respectively then the following conditions are met:
(x1-(ns/2+1)) is greater than or equal to 1.
(x1+(ns/2+1)) is lesser than or equal to nsam.
(y1-(nr/2+1)) is greater than or equal to 1.
(y1+(nr/2+1)) is lesser than or equal to nrow.

.DOCUMENT FILE: DOC001
[Enter the name of the document file where you want the peaks to be stored.]

NOTES

1. This program was written as part of the automatic particle picking program. This program picks out peaks in the filtered and reduced input micrograph and is very efficient in eliminating noise peaks. The peaks are fitted with a gaussian function half-width of which corresponds to the size of the object and so objects whose size strongly deviates from the actual size are rejected.

2. Ref: "Automatic Particle Picking from Electron micrograph" by Lata et.al.

3. Further details: autopartpick.html
   

SUBROUTINES

ATPK, PKD

CALLER

UTIL4