Dear Yu,


If you open the images using the dials.image_viewer command you should see a window called "settings", a screenshot of which I have attempted to attach below.


At the bottoms of the settings window are a number of buttons for seeing how the spot finding algorithm will behave. Clicking any of these will update the display with the following processed image data:


  1.  image - shows the raw image data
  2.  mean - shows the local mean image
  3.  variance - shows the local variance image
  4.  dispersion - shows the local dispersion image
  5.  sigma_b - shows the dispersion threshold mask
  6.  sigma_s - shows the mean pixel threshold mask
  7.  global - shows the global threshold mask
  8.  threshold - shows the combined threshold mask


The "threshold" button shows what the spot finder will consider to be strong pixels on an image.


The various threshold levels can be adjusted in the settings window (sigma background, sigma strong, global threshold, min local, gain and kernel size). Without seeing an image, it is difficult to make specific suggestions; however, playing with these might result in better spot finding.


Finally, in dials.find_spots, some filtering is done to remove e.g. very small and very large spots. If your spots are composed of less than 3 pixels with strong signal, then they will be filtered out. If you could post the contents of the dials.find_spots.log file, it might be possible to see if this is the case.


Best wishes

James


[cid:7a94b8be-c4b3-43ee-8902-7ebe4f4bc455]


________________________________
From: CCP4 bulletin board <[log in to unmask]> on behalf of Zhang Yu <[log in to unmask]>
Sent: 10 April 2018 08:16:36
To: ccp4bb
Subject: [ccp4bb] DIALS spot finding

Dear all,

I am just switching from HKL3000 to DIALS for processing data collected at EIGER detectors because it is too slow for the HKL300 to handle over 1000 images per dataset.

Our crystals are not perfect and you would expect split spots or spots of multiple crystals in most cases. Sometimes we are lucky enough to extract spots of one lattice by playing with the spot-finding parameters in HKL 3000 and find an solution during the index step (changing spot size, more spots, fewer spots, restraining the resolution, etc.). However, it seems very difficult to adjust these parameters in the dials.find_spots step of DIALS.

The DIALS tutorial suggest checking the spots using "dials.image_viewer" after the spot findin step. By inspecting the images, it seems that most split sports were not included into the list of "strong spots" for indexing. What options do you have during the step of spot finding (especially fins strong spots for indexing) using DIALS?

Thank you in advance.
Best,
Yu

--
Yu Zhang
HHMI associate
Waksman Institute, Rutgers University
190 Frelinghuysen Rd.
Piscataway, NJ, 08904


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