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Next: case4.11g/case4.11g.in: output graph-node format Up: Main Menu 4: Analyses Previous: case4.11v/case4.11v.in: output voxel-list format

case4.11cp/case4.11cp.in: output cluster-path format


  

Input Data Options tomographic data (1) segmented data (2) burn data (3) medial axis data (4) throat data (5) Enter choice: 4

Data Processing Options plot MA (1) plot MA with MS (2) convert MS files to segmented file type (3) histogram and fit pore MA burn data (4) embed search tree(s) (5) shortest paths (6) min cut/max flow (7) convert data to/from ascii format (9) convert MA list to node/path formats (10) modify MA (11) histogram MA info (12) throat calculation (13) identify fibers (14) convert to graph format (15) construct neuron (16) reconstruct burn layers (17) isolate neuron soma/dendrite structures (18) Enter choice: 11

Files assumed to be labelled basename.ext, basename is limited to 255 characters maximum, ext is a numerical designator lying between 000 and 999 It is assumed that the files have consecutively numbered extensions ie. 000 -> 056, or 021 -> 049

Enter basename for Medial structure files: ../../Examples/case2.2/lkc_ma_a Are files compressed? [y,n]: y

Resize information selection. NOTE, row and column numbers begin from 0

For each slice, enter first and last column of data to use (x-dir): 0 399 enter first and last row of data to use (y-dir): 0 399

enter first and last slice of data to use (z-dir): 1 5

Trim medial structure voxels on volume edges? (y,n(dflt)): n Enter basename for burn files: ../../Examples/case2.1/burn Are files compressed? [y,n]: y

Medial axis clean up control menu

Maximum burn number on medial axis is 7

Isolated voxel clean up Remove isolated voxels having burn number less than: 2

Isolated path clean up Remove isolated paths having length less than: 8

Branch-Leaf path clean up Remove paths from clusters having coordination numbers in the range c_min <= coord <= c_max Enter c_min, c_max: 0 10 Optional path removal criteria Remove path if length less than maximum cluster burn number (auto) user specified tolerance (user) Enter choice (a(dflt),u): u Remove paths having number of voxels less than: 8

Surface Remnant clean up Reduce surface remant structure where possible(y,n(dflt)): n

Enter voxel length in physical units: 1

Specify output medial axis data format voxel location list only (v) cluster/path format (cp) graph node/path format (g) Enter format (v,cp,g): cp

Merge close clusters? (y,n(dflt)): n Enter basename for singlet loc/burn list files: sngl Enter basename for cluster/path loc/burn list files: cp_loc Enter basename for cluster/path list files: cp_list Are files to be compressed? [y,n]: y



next up previous contents
Next: case4.11g/case4.11g.in: output graph-node format Up: Main Menu 4: Analyses Previous: case4.11v/case4.11v.in: output voxel-list format

Brent Lindquist
Thu Sep 30 12:33:54 EDT 1999