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FindYourCell.jl

Cell Segementation and Tracking

We search and filter local maximal in blurred image as seed, then apply watershed algorithm to split individual cell. Nucleus is extracted by Otsu-threshold in each split region.

Data Structure

cell_info=[x, y, threshold, cell_size, cell_intensity]

Compressed tiff

http://www.graphicsmagick.org/api/types.html#compressiontype http://www.graphicsmagick.org/wand/magick_wand.html#magicksetimagecompression https://github.com/ImageMagick/ImageMagick/blob/2747ccfc1044fc3da6d32ff1ebbca5e926fcf602/MagickCore/compress.h https://github.com/ImageMagick/ImageMagick/blob/2747ccfc1044fc3da6d32ff1ebbca5e926fcf602/Magick%2B%2B/lib/Magick%2B%2B/Include.h Why enum number are wrong?

# hack ImageMagick
function writeimage(wand::MagickWand, filename::AbstractString)
    setimagecompression(wand, 13) # lzw compression
    status = ccall((:MagickWriteImages, libwand), Cint, (Ptr{Cvoid}, Ptr{UInt8}, Cint), wand, filename, true)
    status == 0 && error(wand)
    nothing
end