Introduction
ISee! is able to perform a so-called "flat field" correction and the correction of bad pixels. In order to do it:
- A sequence of uniformely illuminated images has to be taken as the first step. They are called tion or reference images. The exposures have to be done without an object. All setup-variables have to be the same as with the object, except the number of frames to be integrated - it has to be 3-5 times higher for the correction images. Mean intensities of these images have to range from the minimum till the maximum representable value, i.e. cover whole dynamic of the detector.
- Create a configuration file. Essentially it is a list of reference images, stored as plain ASCII-text, one filename per line, ordered from the darkest (dark image) to the brightest. It is used by ISee! for fine adjusting of the grey values of individual pixels in real (i.e. with object) shots. If an acquisition system is inherently and highly linear, then only two (black and white) correction images are enough. Otherwise (for a nonlinear system) more correction images are necessary since 1st order (linear) interpolation is used between corrected grey values. An extensive example of a configuration file with all options explained is shown below.
Example Configuration file
You can download the following configuration file from here.
# This is an example "ISee! Pixel and Bad Pixel Correction" configuration file. # All possible (as for ISee! v1.7.4 and above) options/commands are listed and explaned. # Lines starting with sharp character (#) are considered as comments and ignored by ISee! # Written by Alexander Alekseychuk (alexander.alekseychuk@bam.de), 2008-11-15 # List reference images in order of ascending exposure (average grey value). # The number after image filename is optional and specifies target grey value of this reference. # If ommited, ISee! will calculate and use the image' global median for the target grey value. black.tif 0 0.02mA.tif 200 0.05mA.tif 500 0.10mA.tif 1000 0.19mA.tif 1900 0.38mA.tif 3800 0.75mA.tif 7500 #1.50mA.tif 15000 # Perform correction so that the black-image will have grey value of zero after correction. # In other words: image will be corrected for the offset. # Then the first image in the list above will be considered as a reference black-image. $adjust_black # Default interpolation between reference images is linear, i.e. 1st order. # This option enables 2nd order interpolation. Seldom necessary, # unkomment only if you really need this. #$use_2d_order # Detection of bad pixels by analysis of their gain. # # The first number (argument) is global sensitivity. It is the allowed deviation of gain # of each single pixel from the global median gain, expressed in standard deviations. # # The second number is local sensitivity and it is the allowed gain deviation from the # median gain in 21x21 local area (local area size is according to E2597). If set to zero # or a negative number - no local analysis is performed (_significantly_ faster). #$detect_bad_pixels 5.0 3.0 $detect_bad_pixels 5.0 -1 # Detection of bad pixels by means of correction (grey value adjustment) of a reference image # and detection of pixels which cannot be corrected sifficiently good. # # Remenber to comment out the corresponding images in the list of reference images (above). # # The second (numerical) parameter is the allowed deviation of grey value in the corrected image # from the median grey value in 9x9 local area (local area size is according to E2597), # expressed in _percents_. #$detect_bad_pixels 0.10mA.tif #$detect_bad_pixels 0.38mA.tif 1.5 # In case if bad pixel detection resulted in a excessive number of detections, this option # allows to set a warning signal. The argument is the percentage of bad pixels in relation # to the number of all pixels (image size). $bad_pixels_high_sens_warn 10 # Once succesively detected bad pixels have to be saved in a file, bad pixel map, # in order to be reused after that since the bad pixel detection procedure is time consuming #$save_bad_pixels_map bad_pixels.tif # And this command allows to load the bad pixel map saved before. #$bad_pixels_map bad_pixels.tif # Commands ISee! to ignore possible interferences between bad pixels and their immediate neighbours. # Leave it commented out, if you have no good reason to do the opposite. #$ignore_pixel_leakage # # eof
Documented correction example
You can download a complete documented ready-to-use package with example configuration files and images (17.8 MByte).
