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dagewa / DIALS_for_ED_paper

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R1Q1 Spot finding #13

Closed dagewa closed 6 years ago

dagewa commented 6 years ago

Comments on spot finding:

dagewa commented 6 years ago

Noise level: I don't know if this refers to detection noise (i.e. response and read noise) or background level. It might be worth reiterating that the Timepix is a counting detector. That may not be clear enough in this text.

dagewa commented 6 years ago

Algorithm of spot finding: explained in detail here: https://journals.iucr.org/d/issues/2018/02/00/di5011/. Short reply to that effect:

"The spot-finding algorithm is based upon the method used by XDS and is described in detail in section 3.1 of the main DIALS reference (https://journals.iucr.org/d/issues/2018/02/00/di5011/). Pixels exceeding a local threshold are marked as strong, and spots are formed by connecting strong pixels in 3D."

dagewa commented 6 years ago

Width of peaks: additional comment as follows: "The width of spots, background level and various detector properties are all relevant factors for success in spot-finding. As described in Section 2.2 we advocate trial and error optimisation of spot-finding settings, which is made easy interactively within the dials.image_viewer"

dagewa commented 6 years ago

Reply: There are more details about the camera in Clabbers et al. (2018) and references cited therein, however it is useful to clarify here that the detector operates in counting mode and thus has Poisson response (but with a multiplicative gain of exactly 3, for the reasons described in the text). We have added that note. The spot-finding algorithm is based upon the method used by XDS and is described in detail in section 3.1 of Winter et al. (2018). Briefly, pixels exceeding a local threshold are marked as strong, and spots are formed by connecting strong pixels in 3D. We feel it is unnecessary to repeat the details here. The width of spots, background level and various detector properties are all relevant factors for success in spot-finding. Typical spot widths vary greatly even for X-ray data: compare for example images recorded on CCD detectors with significant point-spread vs HPAD counting detectors. The algorithms used by XDS and DIALS are applicable over a wide range of cases, with appropriate selection of user parameters. As described in Section 2.2 we advocate trial and error optimisation of spot-finding settings, which is made easy interactively within the dials.image_viewer.