Some software enables overlay of a batch of images so that you simulate the classical crude phi slicing and get visible patterns. I think we tried with d*Trek.
Jan On Tue, Apr 28, 2015 at 9:20 AM, Graeme Winter <[email protected]> wrote: > Looking at PAD images is something we have had to get used to at Diamond, > and sometimes it takes some tweaking to get a really good idea of what the > images actually look like. This is a challenge if you measure the data > properly with fine slicing & low dose... > > One thing which really helps is to have the positive image rather than the > negative i.e. white spots on a dark background. The eye is much better at > picking these out. There are also tweaks which can be done within image > viewers to make spots more visible for example showing the maximum rather > than average of an n x n zoomed out image. ADXV white on black background + > 100% scale generally works well. Summing the images using e.g. XDS > merge2cbf or dials.merge_cbf can make them easier to interpret, > particularly if you're used to looking at 1 degree CCD images. > > Within dials (http://dials.sf.net) we have an image viewer, > dials.image_viewer, which also has the option to calculate local mean, > variance, dispersion and so on so you can see "what the spot finding sees" > - this can make a massive difference. For example: > > Default image > > > http://www.ccp4.ac.uk/xia/screenshots/Screen%20Shot%202015-04-28%20at%2008.01.34.png > > Tweaked to "inverse" i.e. right way around, brightness turned down: > > > http://www.ccp4.ac.uk/xia/screenshots/Screen%20Shot%202015-04-28%20at%2008.01.52.png > > - much better - but then the dispersion map thresholded a la spot finding: > > > http://www.ccp4.ac.uk/xia/screenshots/Screen%20Shot%202015-04-28%20at%2008.02.06.png > > This really shows the images well... also allows you to tweak the spot > finding settings nicely. This is a particular problem with good crystals > from a good beamline as the spots can often be 1 or 2 pixels with many many > counts on a background of very small (often 0) counts. > > A final challenge with these detectors is that they *actually count > photons* i.e. the statistics are the same as counting cars going past the > school* - where on a CCD if you can *see* a spot there is a spot there, as > it's climbed out through the readout noise etc, on a PAD you need to look > at the numbers and by and large put more faith in the processing software > than your eyes, as people are great at finding patterns where no patterns > are there to be found. > > Flip side is yes, the images are harder to interpret but these detectors > do a nice job of actually recording diffraction! > > best wishes Graeme > > > > ------------------------------------- > *other elementary examples exist. > > > > On Tue, Apr 28, 2015 at 3:08 AM Jens Kaiser <[email protected]> wrote: > >> SSRL Bluice opens the image in adxv upon double click in the diffraction >> window. >> >> HTH, >> >> Jens >> >> On Mon, 2015-04-27 at 16:57 -0700, Bernhard Rupp (Hofkristallrat a.D.) >> wrote: >> > Thanks - particularly great if we had these images/option available to >> look >> > at >> > in real time during data collection, w/o first having to download the >> raw >> > data (not >> > really feasible during remote data collection). I don't think the ESRF >> > online data base has the option, but other beam lines may? >> > >> > Thx, BR >> > >> > -----Original Message----- >> > From: James Holton [mailto:[email protected]] >> > Sent: Monday, April 27, 2015 4:05 PM >> > To: [email protected]; [email protected] >> > Subject: Re: [ccp4bb] PAD images >> > >> > >> > In the ADXV viewer: >> > http://www.scripps.edu/tainer/arvai/adxv.html >> > >> > Go to Edit:Settings and click on the "Small Spots" radio button. This >> solves >> > most of the "I can't interpret the spots" problems you describe. >> > >> > -James Holton >> > MAD Scientist >> > >> > On 4/27/2015 3:31 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: >> > > Hi Fellows, >> > > >> > > I wonder whether it's just me and my eyesight failing (or excessive >> > > internal lubrication).... >> > > >> > > It seems that the art of looking at diffraction patterns and being >> > > able to tell a lot about modulation, superstructures, extinctions, >> > > etc. becomes kind of useless old fart stuff when dealing with PAD >> > > images. I can't for my life see interpretable patterns on frames >> > > where the beamline autoprocessing delivers actual data sets. The >> > > absence of a point spread function etc that gave interpretable >> > > film-like images on IPs or CCDs, seems to be the reason. >> > > >> > > A PAD pixel with 1000000 counts looks like one with 100 when viewed >> > > with the low dynamic range of the displays compared to the huge >> > > dynamic range of the detector. >> > > >> > > Is there somewhere in the process a humanly unusable composite image >> > > with a point spread that allows visual pre-processing, inspection, and >> > > interpretation despite a low dynamic display range? >> > > >> > > Looking at the hklview or similar after processing is pointless (no >> > > pun intended), because the stuff I might be interested in is already >> > > processed away. >> > > >> > > Some humanly interpretable raw data images would be quite useful... >> > > >> > > Best regards, BR >> > > ----------------------------------------------------------------- >> > > Bernhard Rupp >> > > 001 (925) 209-7429 >> > > +43 (676) 571-0536 >> > > [email protected] >> > > http://www.ruppweb.org/ >> > > ----------------------------------------------------------------- >> > > The man who follows the crowd will get no further than the crowd. >> > > The man who walks alone will find himself in places where no one has >> > > been before. >> > > ----------------------------------------------------------------- >> > -- Jan Dohnalek, Ph.D Institute of Biotechnology Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 +420 226 201 571 Fax: +420 296 809 410
