Input Data Options
	special purpose data requiring pre-processing (0)
	tomographic data (1)
	segmented data (2)
	burn data (3)
	medial axis data (4)
	throat data (5)
	fluid data (6)
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)
	construct fish (8)
	convert data to/from ascii format (9)
	convert MA list to/from 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: ../ma/oil
Are files compressed? [y,n]: y

Enter basename for burn files: ../burn/oil
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 99
   enter first and last row of data to use (y-dir): 0 99

enter first and last slice of data to use (z-dir): 1 100

Trim medial structure voxels on volume edges? (y,n(dflt)): y
9828 ma voxels read in
9828 ma voxels after resize
2049 ma voxels on boundary initially. 1752 bdry ma voxels removed

Medial axis clean up control menu

	Maximum burn number on medial axis is 11

    Remove isolated voxels (y,n(dflt)): y
	Remove isolated voxels having burn number less than: 12

    Remove isolated paths (y,n(dflt)): y
	Remove isolated paths having length less than: 100

    Remove branch-leaf paths (y,n(dflt)): y
    Retain branch-leaf paths exiting through boundary? (y,n(dflt): n
    branch-leaf path removal criteria
	Remove path if length less than
		maximum cluster burn number (auto)
		user specified tolerance    (user)
	Enter choice (a(dflt),u): user
	Enter tolerance length: 100

    Remove needle-eye paths (y,n(dflt)): y
    needle-eye path removal criteria
	Remove path if length less than
		maximum cluster burn number (auto)
		user specified tolerance    (user)
	Enter choice (a(dflt),u): u
	Enter tolerance length: 100

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

Enter voxel length in physical units: 4.1

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)): y
Select the criterion for merging clusters. Two clusters
will be merged if they are separated by a path
	a) having length (measured in voxels) less than the
	maximun burn number at either end of the path + 2
	b) having minimum interior burn number greater than
	or equal to the minimum burn number at either end
	c) having length (measured in voxels) less than
	a value specified by the user.

Specify criterion (a(dflt),b,c): a


Enter basename for singlet loc/burn files: ../ma_t/cp_sngl
Enter basename for cluster/path loc/burn files: ../ma_t/cp_loc
Enter basename for cluster/path structure files: ../ma_t/cp_struct
Are files to be compressed? [y,n]: y