MRCFile.jl implements the MRC2014 format for storing image and volume data such as those produced by electron microscopy. It offers the ability to read, edit, and write MRC files, as well as utility functions for extracting useful information from the headers.
The key type is MRCData, which contains the contents of the MRC file, accessible with header and extendedheader.
MRCData is an AbstractArray whose elements are those of the data portion of the file and can be accessed or modified accordingly.
using Pkg
Pkg.add("MRCFile")This example downloads a map of TRPV1 and animates slices taken through the map.
To set-up this example, install FTPClient and Plots with
using Pkg
Pkg.add("FTPClient")
Pkg.add("Plots")using MRCFile, FTPClient, Plots
emdid = 5778 # TRPV1
ftp = FTP(hostname = "ftp.rcsb.org/pub/emdb/structures/EMD-$(emdid)/map")
dmap = read(download(ftp, "emd_$(emdid).map.gz"), MRCData)
close(ftp)
dmin, dmax = extrema(header(dmap))
drange = dmax - dmin
anim = @animate for xsection in eachmapsection(dmap)
plot(RGB.((xsection .- dmin) ./ drange))
end
gif(anim, "emd-$(emdid)_slices.gif", fps = 30)
MRC files can be huge. It is convenient then to load their data as memory-mapped arrays. This is easy to do:
using MRCFile
path = "mymap.mrc" # path to large uncompressed MRC file
mrc = read_mmap(path, MRCData)
... # do somethingNote that writing to memory-mapped arrays is currently not supported.
mrcfile is a full-featured Python implementation of of the MRC2014 format.