FixBadPixel takes a list of points and an image stack and for each point in the list replaces the value at the point by a value interpolated from two of its neighbors in the same section. When points in the list are adjacent, the algorithm attempts to interpolate from points not in the list and, when that is not possible, to do a series of interpolations (first for the points in the list which can be interpolated from points not in the list and then for those that are successively farther away from such points). When such a series for all points in the list could not be found, a warning will be displayed.
The list of points is simply a text file with one line per point and each line with the x, y, and z pixel coordinates. There can be extra comment or header lines; such lines are ignored if they don't begin with something that could be interpreted as three numeric values. Pick Points or Find Points are two applications that could be used to generate the list of points.
FixBadPixel's user interface uses the same set of controls for selecting and processing a region as other Priism applications. There are additional controls, the "PList" button and adjacent text field, for selecting the point list file. The "Num Iteration" field sets how many times to repeat the set of interpolations on a given section; just leave its value at one since repeating the process with the current algorithm doesn't give different results and takes more time.
Apply Calibration also includes a bad pixel editing option, but it uses a simpler algorithm (simple replacement by another nearby value) and expects a point list in the format generated by the OM data collection software, Resolve 3D. Bad pixel editing is typically done before using CCDCor to correct for systematic intensity variations or deconvolving the data.
Overview | Region processing | Number of iterations
Apply Calibration | Pick Points | Find Points | CCDCor | Decon | Priism
FixBadPixel first interpolates the intensity at points in the input list which have at least two neighbors that are not in the list. Then it interpolates those points which have at least two neighbors which either weren't in the list or were interpolated in the first batch of interpolations. This is repeated until all the points in the input list have been handled.
To repeat the series of interpolations, use a value greater than one in the "Num Iteration" field. With the current algorithm, the results are the same when the interpolations are repeated so there is no reason to use a value other than one.
Overview | Region processing | Number of iterations