Leginon

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 pixel, a column/row]] or a [[Bright and Dark reference images#Bad-Region-Correction|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.

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.

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[[Pixel Size Calibration|< Pixel Size Calibration]] | [[Image Shift matrix calibration|Image Shift matrix calibration >]]

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