Bright and Dark reference images » History » Revision 11
Revision 10 (Amber Herold, 06/23/2010 12:48 PM) → Revision 11/24 (Amber Herold, 06/23/2010 12:53 PM)
h1. Bright and Dark reference images Bright and Dark reference images need to be acquired for every camera setting that will be used. The camera settings include image dimension, bin size, and offset. Over time, references may need to be repeatedly acquired. h2. Correction Channels When two flat-field-corrected images are correlated, there is often an origin peak derived from the common normalization image even if both image acquisition contains only noise. In order to avoid this problem, two or more sets of bright/dark references, and hence normalization images can be obtained per CCD camera configuration. When a correlation between two images will be done, Leginon will check the channel of the correction the first acquired image has used and then force the new image to be corrected by a different channel. To use this function, simple set the number of channels to 2 or larger in Correction/Settings/Image Correction/Reference Creation> while creating the reference images. h2. Acquire reference images * scope> make sure that the CCD will be acquiring images in an area with uniform beam intensity such as an empty area with no specimen nor support. You may skip a trip to the scope room by sending one of the high mag preset to the scope from Leginon. * Leginon/Node Selector> Select "Correction" node. * Leginon/Correction/Toolbar> Open "Settings" window. * Leginon/Correction/Toolbar/Settings> Select one of the Common Camera Configuration or select Custom mode and enter your own values based on the presets you created. * Leginon/Correction/Settings/Camera Configuration> Enter the Exposure time. It should be chosen so that the image is not saturated and ideally close to the condition that will be used in the experiments. If unsure about the experimental condition, use an exposure time that gives high but not saturated counts. * Leginon/Correction/Settings>By default, the corrector node is set to average 3 images together to create one reference image and to despike the hot pixels with averaged neighbor hood values. These can be changed if desired. * Leginon/Correction/Settings> It is recommended to use 2 [[Bright and Dark reference images#Correction-Channels|correction channels]] for the camera configuration used for correlation peak search. * Leginon/Correction/Settings> Click OK to exit settings. * Leginon/Correction/Toolbar> Select "Raw image " from the pull down list of acquisition modes and then click on "Acquire" button next to the selector to view an image that is not corrected. * Leginon/Correction/Toolbar> Select "Dark reference" in the acquisition mode selector and then click "Acquire" to acquire the Dark reference image for this particular camera configuration. * Leginon/Correction/Toolbar> Select "Bright reference" and repeat the acquisition to obtain the Bright reference. * Leginon/Correction/Toolbar> Select "Corrected image" and then "Acquire" to view the corrected image. A corrected image should be free of artifacts and have smaller standard deviation than the raw image, in general. * Repeat steps 3-11 for all the images and bin sizes that will be used: * If [[Bright and Dark reference images#Correction-Plan|a images#Image-Despike|a pixel, a column/row]] or a [[Bright and Dark reference images#Bad-Region-Correction|region]] images#Image-Despike|region]] gives bad values in the bright or dark image after a few trials, it may be excluded in all corrected images. * Only one channel is required for image shift alignment purpose. If the same camera configuration is used for presets that involves in correlation, two channels are strongly recommended. Bright/Dark Reference Image Need for the Example MSI: |*Dimension after binning*|*Bin*|*number of correction channels*| |4096|1|1 or 2 if used for tomo preset| |1024|4|2^*^| |1024(centered)|1|1^**^| |512|8|2^***^| |512 (centered)|1|1^***^| ^*^-This camera configuration is used in preset beam shift alignment even if you don't use it for a preset. ^**^-This camera configuration is used in Manual Application Manual Focusing even if you don't use it for a preset. ^***^-These camera configurations are used in preset image shift alignment even if you don't use it for a preset. h2. Image Despike The Despike feature removes random bright or hot pixels from the acquired images. This hot pixel is assigned the average intensity of the surrounding area, a circle of the radius which is entered in Neighborhood Size. The Despike Threshold is the number of standard deviations away from the mean that qualifies a pixel for despike correction. The despike affects the flat-field corrected image saved on the disk and can not be recovered. Therefore, use a minimal neighborhood size to avoid artifact and set the threshold high to avoid over-despiking. over-dispiking. Activation of this feature and its parameter settings are defined when in the pop-up dialog for "Edit Correction Plan". See below. h2. Correction Plan Bad Pixel, Rows and Bad Cols are used to crop portions of the image that do not read well off of the CCD. The values entered into here are determined empirically for each instrument that Leginon operates on. If one column or row of the images is incorrect, measure the location of the row and column that need to be removed from this image. These values should then be entered as a sequence of values separated by commas by editing the Plan. Click Save after adjusting. Individual bad pixel can also be corrected by its surrounding pixels. Choose these pixels with the selection tool on the image and then click on "Grab From Image". h2. Find A Single Bad Pixel When a single pixel is defected, it may not be easy to find it on a large image, even if it changes the stats dramatically. A tool is available to help finding these pixels: * Leginon/Correction> Acquire either a corrected image that shows the bad stats. * Leginon/Correction/Toolbar> Left-click on the !http://emg.nysbc.org/software/leginon/images/icons/stagelocations.png! button to "Add extreme points to bad pixel list". There * Leginon/Correction/Tools> Left-click on the "Add Region" tool that looks like "+". This adds the selected bad region to the bad pixel plan. * Leginon/Corrections> Acquire a corrected image in the same configuration to check if the apearance improves. h2. Bad Region Correction When a large region is covered by a fallen chip, image correction through bright/dark reference may not be sufficient to produce a spike-free image since the bright and dark values in the region are almost identical. To add such a large region into bad pixel plan, do the following: * Leginon/Correction> Acquire either a bright or corrected image that shows the bad region clearly. * Leginon/Correction> Use "Regions" target tool next to the image to enclose the bad region. The corners that the target tool identifies can be larger than the bad region but should be close to its size so that not too much is corrected. * Leginon/Correction/Tools> Left-click on the "Add Region" tool that looks like "+". This adds the selected bad region to the bad pixel plan. * Leginon/Corrections> Acquire a corrected image in the same configuration to check if the appearance improves. ______ [[Pixel Size Calibration|< Pixel Size Calibration]] | [[Image Shift matrix calibration|Image Shift matrix calibration >]] ______