Leginon

h1. Corrector

Corrector handles image corrections before it is displayed and saved. It has three

functions:

*  Create the normalization images by acquiring bright/dark reference images.

*  Upon the request by another node, load the normalization image from the requested

channel and perform the flat-field correction.

*  Perform addition corrections such as despiking, intensity clipping, and specific

pixel/column/row intensity correction to the flat-field corrected image above.

<highlights>

Required bindings: None

</highlights>

h2.  Normalization Image

Flat field correction removes the contribution of dark current to the intensity and

artifacts on the CCD camera that are reproducible, for example, the patterns of the fiber

optic plate and debris fall and remain stationary on the CCD.

Dark images record the residual intensity recorded by the CCD for the same length of

acquisition time as the chosen camera configuration but with no electron beam present.

Bright images record the raw image under the same condition except that the camera is

flooded with uniform electron beam.

Let the mean of an image be avg(Image)

Normalization_Image_Pixel_Value = [avg(Bright_Image-Dark_Image)]/(Bright_Pixel

-Dark_Pixel)

Flat-Field_Corrected Image_Pixel_Value = (Raw_Image_Pixel_Value) *

(Normalization_Image_Pixel_Value)

Some Leginon functions requires more than one image, for example the cross/phase

correlation done in drift monitoring of Drift Manager node. When the node acquires a new

image that will be used to correlated to an old image, it checks the correction channel that

the old image used, and force the new image to use a different correction channel. This

process eliminates the origin correlation peak produced by identical noise in the two images

when the same correction channel is used.

h2.  Settings for Creating the Normalization Image

* Instrument and Camera Configuration

Best to use an exposure time/intensity similar to the data acquisition

* Images to combine

* Combine method = averge|median

Both methods are applied per pixel. Averge is used normally. Medium is used when

x-ray spikes are a common problem and requires a larger number of combining

images.

* Number of Channels = the numbers of separate normalization images that will be

saved for the camera configuration.

h2.  Settings for Image Flat-Field Correction from Another Node

* No settings are required. If normalization image does not exist for the camera

configuration, there will be no correction. Channel selection is also

automatic.

h2.  Correction by the correction plan

Correction plan is a list of bad columns, rows, and pixels that tend to give

non-repeating error readings. A good example is often found at the last columns of the CCD.

Because their non-repeating nature, flat-field correction can not remove their

contribution.

The correction plan is associated to individual instrument, camera, and camera

configuration.

*  Edit Plan = Add/Edit/Delete the bad columns/rows/pixels. Separate values by

commas and pixel coordinates should be in ( ). For example, a bad pixel list may be

entered as (10,20),(11,20),(11,21).

*  Grab from Image = Grab bad pixels marked in red on the image displayed.

h2.  Intensity Clipping and Image Despike

Intensity clipping and image despike are done after flat-field correction. Intensity

clipping simply replace pixel values that is outside the min/max range with the limits.

Despike defines a hot pixel as a pixel that has intensity higher than the threshold

multiples of standard deviation above the mean of a neighborhood box. The intensity of the

hot pixel is replaced by the mean of the neighborhood box.

h2. Related Settings

The settings related to these two corrections apply to all camera configuration and

images passed through Corrector.

* Clipping Max | Min

* Despike Neighborhood Size (pixel): An input of 11 gives a box of 11x11 centered

at the pixel where spiking is evaluated.

* Despike Theshold (x standard deviation above the mean of the neighborhood box

(For example 11x11=121 pixels))

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 <inlinegraphic

fileref="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 apearance improves.

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[[Click Target Finder|< Click Target Finder]] | [[Dose Calibrator|Dose Calibrator >]]

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