AT PK - Automatic particle picking - peak search

(10/30/13)

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.   Example.

SEE ALSO

AT WN [Automatic particle selection]
AT SA [Automatic particle picking - statistical parameters ||]
AT IT [Automatic particle picking - sort doc file]

USAGE

.OPERATION: AT PK

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

.PIXEL NEIGHBORHOOD FOR SEARCH: 13
[Enter the number of pixels which corresponds approximately to the size of the particle. For the above input of: 13, the filtered image is searched to find the highest peak in a 13 by 13 square. In this way picking the same particle is avoided and also the nearest neighbour distance is taken into account. Must be >= 3.]

.CC 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 X1 and Y1 are the X- and Y- coordinates of the peaks, and nxe, nye, are the dimensions of the micrograph edge, and nx and sy are the dimensions of the micrograph, then the following conditions are met:
(X1-(nxe/2+1)) is >= to 1.
(X1+(nxe/2+1)) is <= to nx.
(Y1-(nye/2+1)) is >= to 1.
(Y1+(nye/2+1)) is <= to ny.

.PEAK LOCATION DOC FILE: DOC001
[Enter the name of the document file where you want the peaks to be stored. The peak positions (relative to origin) will be printed in the document file as follows:

  Peak number   Y

NOTES

  1. This operation was written as part of the automatic particle picking program. It picks out peaks from a shrunken, filtered 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

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