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clem_align: finding the correspondences

Interactive function to find coordinate transform from fluorescence to EM image

Next, the program starts the peak searches and opens up a new window for determining the right number of peaks for the EM image.

running peak searches

 find number of peacks for EM

 click in the slider (do NOT slide) to determine threshold

 wait until image update is finished before clicking again

 type 'r' and hit return to redo picking

 hit return in this terminal window once done 

clem-em-peaks-start

In this case, there are too many peaks assigned. One would want to have the majority of peaks on complete circles and not on circles that are partially obscured or not completelyin thepicture. Adjust the number of peaks by clicking on the slider until satisfied.

clem-em-peaks-end

Once satisfied, go to the terminal window and hit return. 

 number of peaks: 40

The program will report the number of peaks and then commence to run a full-blown peak search to determine accurate hole centers (which may take a while). After this is finished, the same procedure is invoked for the fluorescence image.

clem-fl-peaks-start

 find number of peacks for fluorescence

 click in the slider (do NOT slide) to determine threshold

 wait until image update is finished before clicking again

 type 'r' and hit return to redo picking

 hit return in this terminal window once done 

clem-fl-peaks-end

 number of peaks: 33

Once the calculation is finished, the correspondence picker window will open.

clem-correspondence

starting hole correspondence picker

 click in grey area to delete last entry

 hit return in this terminal window when done

The fluorescence image is now rotated by the angle specified when calling 'clam_align'. This makes the picking of the correspondences easier. Pick a few correspondences by clicking first on a white box in the left panel and then on the corresponding box in the right panel. Repeat for a few times (you will need a minimum of two but 3-5 is recommended).

picking   16 ->  21

picking   14 ->  28

picking   17 ->  27

picking   19 ->  26

When done, go to the terminal window and hit return.

 

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