mia-2dseries2dordermedian {-i string} {-o io} [ options ...] [ Plugin type: 2dimage/filter ...]


This program evaluates the pixel-wise median of the absolute values of the gauss filtered 2nd order temporal derivative of a series of images. In addition, it can be used to output the time-intensity curve of a given pixel.The program supports slice-wise spacial pre-filtering by giving additional filters as free parameters (filter/2dimage).


-i, --in-file=(input, required); string

input segmentation set

-o, --out-file=(required, output); io

output image name. For supported file types see Plugin type: 2dimage/io

-k, --skip=0; ulong

Skip files at the beginning

-e, --enlarge-boundary=5; ulong

Enlarge cropbox by number of pixels

-c, --crop

crop image before running statistics

-g, --gauss=1; ulong

gauss filter width for moothing the gradient


intensity time curve output file

--itc-loc=[0,0]; 2dbounds

intensity time curve output pixel coordinates

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

debug:Debug output
message:Normal messages
info:Low level messages
error:Report errors
fatal:Report only fatal errors
trace:Function call trace
fail:Report test failures
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit


--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).


Evaluate the median of the 2nd order derivative of the series given in segmentation set segment.set after filtering with a Gaussian of width 3. In addition write the time intensity curve of pixel <128,64> to curve.txt.

mia-2dseries2dordermedian -i segment.set -o gradmedian.exr -g 1 --itc-file curve.txt --itc-loc "<128,64>"


Gert Wollny