Given a set of raw 3D tiff stacks from the microscope and a tilebase.cache.yml file containing the stitching parameters, use barycentric transforms to generate an octree for viewing with the Janelia Workstation.
Julia, version >=1.3, plus the Cairo, Colors, Gadfly, HDF5, ImageMagick, Images, JLD2, Morton, and YAML packages.
Nathan Clack's mltk-bary library.
Tested with Julia v1.7.1, Cairo v1.0.5, Colors v0.12.8, Gadfly v1.3.4, HDF5 v0.15.7, ImageMagick v1.2.2, Images v0.25.0, JLD2 v0.4.17, Morton v0.1.1, YAML v0.4.7, and mltk-bary master/84e15364.
Install the mltk-bary library using make.sh.
Be sure to edit rootdir and installdir therein appropriately.
Download the latest precompiled binary of Julia. Install
the required packages by changing to the directory of the render repository,
starting Julia on the unix command line, entering Pkg mode by pressing ],
and then invoking the activate ., instantiate and precompile commands.
To install into a shared system directory, instead of your home directory,
preceed these commands by popfirst!(DEPOT_PATH).
Make sure that RENDER_PATH, LD_LIBRARY_PATH, JULIA,
and JULIA_PROJECT in render, monitor, and project
are all set appropriately.
First, set the desired parameters by editing a copy of src/parameters.jl. At a minimum, the source variable should point to the full path of the tilebase.cache.yml file and the destination variable to the directory in which to save the octree.
Start the render as follows:
ssh login1
cd /groups/mousebrainmicro/mousebrainmicro/Software/barycentric/src/render
./render <copy-of-parameters.jl>
To watch its progress check the tail of the monitor.log file.
Should you kill the render, or in case it crashes or hangs before it finishes, be sure to delete all the temporary files on the cluster nodes:
./janitor <destination>
There is also a utility to create 2D projections from a 3D octree. As with the renderer, the settings are stored in a file, src/projection-parameters.jl.
src/project <copy-of-projection-parameters.jl>
More detailed documentation is at the top of each source code file.
tilebase.cache.yml
homography is now deprecated, and use to contain an affine transformation matrix before barycentric transforms were used instead
dims is the size of the input tiles in voxels
{x,y,z}lims specifies how to crop and partition the input tiles in voxels. a barycentric transform is applied to each partition
coordinates specifies in nanometers the desired output position of each node in the partition. if there is just one partition, there should be 8 (nodes/corners) x 3 (dimensions) = 24 numbers. more generally there are length(xlims)*length(ylims)*length(zlims) nodes. the order of the numbers is as follow:
x1_n1, y1_n1, z1_n1, x2_n1, y1_n1, z1_n1, x1_n1, y2_n1, z1_n1, x2_n1, y2_n1, z1_n1, x1_n1, y1_n1, z2_n1, x2_n1, y1_n1, z2_n1, x1_n1, y2_n1, z2_n1, x2_n1, y2_n1, z2_n1, x1_n2, y1_n2, z1_n2, ...
and then repeat for node 2 (n2)
ori is the minimum in each column of coordinates; shape is maximum in each column minus the minimum.
If a squatter hangs, you can spoof its communication and get the director to continue with the inter-node merge by:
julia> sock = connect("<director_name>.int.janelia.org",2000)
TcpSocket(open, 0 bytes waiting)
julia> println(sock,"squatter <squatter_num> is finished")
To run a peon manually,
julia> using Sockets
julia> server = listen(IPv4(0),2001)
Sockets.TCPServer(RawFD(18) active)
julia> accept(server)
and then in bash execute the peon.jl script with all of its arguments.
Ben Arthur, arthurb@hhmi.org Scientific Computing Janelia Farm Research Campus Howard Hughes Medical Institute
