Stereotaxic editor
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StereotaxicEditorRAMON.app/Contents
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README.md

README.md

StereotaxicRAMON

General commands

commands
List all commands
help(name)
Print help on command a command
penSize(size_in_pixels)
Arg[1]=size in pixels
setMouse(mouse_mode)
Change mouse mode to arg[1]={sample,paint,select,cselect,poly,fill}

Commands acting the volume data

abs
Absolute value
addConstant(value)
Add 'value' (a float number) to the volume values
multiplyConstant(value)
Multiply the volume values by arg[1]
applyRotation
Apply current rotation
boxFilter(filter_size,iterations)
Arg[1]=filter size, arg[2]=iterations
changePixdim(dim_x,dim_y,dim_z)
Change voxel dimensions in the header
convertToMovie(path)
Convert slices into mp4 movie stored at path arg[1]
crop
Crops volume to the bounding box of the selection
mode
Change value of each voxel in the selection by the mode of a neighbourhood of size 7x7x7
polygonize(path)
Save a mesh of the selection at arg[1]=path
reorient(new_orientation)
Change the current 'xyz' orientation of the volume to that of the string in arg[1], for example, zxy
resample(x_dim,y_dim,z_dim,interpolation)
Resample volume to pixel dimensions arg[1-3], using arg[4]={nearest,trilinear} interpolation
resize(x_dim,y_dim,z_dim,justification)
Resize volume to dimension arg[1-3], arg[4]=three characters containing the justification flags s=start, c=center, e=end for the x, y and z dimensions (for example ssc=x start, y start, z center)
save
Overwrite volume
saveAs(path)
Save data volume at arg[1]=path
savePicture(path)
Save current image at arg[1]=path
set(value)
Set the selected voxels to 'value'
setRotation(x_rotation,y_rotation,z_rotation)
Rotate the volume arg[1-3]=angle x, y, z, in degrees
setVolume(path)
Reload volume
stdev(neighbourhood,maximum)
Replaces volume by the local standard deviation of its values, clipping the maximum

Mathematical morphology operators

dilate(size_in_voxels)
Dilate selection arg[1]=number of voxels
erode(size_in_voxels)
Erode selection arg[1]=number of voxels
tpDilate(size_in_voxels)
Topology-preserving dilate selection arg[1]=number of voxels
tpDilateOnMask(size_in_voxels,path_to_mask)
Topology-preserving dilate selection inside a mask, arg[1]=number of voxels, arg[2]=path a mask with the same dimensions as the current volume
tpErode(size_in_voxels)
Topology-preserving erode selection arg[1]=number of voxels

3D Fourier transform

dct
Direct cosine transform
idct
Inverse discrete cosine transform

Measure

minMax
Print minimum and maximum values
histogram
Histogram of volume's selected values
info
Display file header information
stats
Prints summary statistics of the selection

Commands acting on the selection

addSelection(path)
Add selection from arg[1]=path
loadSelection(path)
Load selection at arg[1]=path
saveSelection(path)
Save selection at arg[1]=path
subtractSelection(path)
Subtract selection from arg[1]=path
boundingBox
Select the smallest box including all currently selected voxels
box(xmin,ymin,zmin,xmax,ymax,zmax)
Select the region inside the box arg[1-6]=xmn,ymn,zmn,xmx,ymx,zmx
connectedSelection(x,y,z)
Keeps only the selection connected to coordinate x,y,z
deselect
Clears the selection
euler
Display Euler's characteristic for the selection
fill(x,y,z,plane)
Fills in 2D starting at coordinates arg[1-3]=x,y,z in plane arg[4]=X, Y or Z
grow(min,max)
Add to the actual selection connected voxels with values between arg[1,2]=min,max
make26
Remove edge and corner neighbours so as to make the selection 26 connected
invert
Invert selection
select(x_coord,y_coord,z_coord,min_value,max_value)
Select voxels around x_coord,y_coord,z_coord with values within min_value and max_value
setThresholdWidth(width)
Expand the threshold to include values within the width
smooth(threshold,n_iterations)
Smooth selection by removing all voxels with less than threshold, for n_iterations
threshold(value,direction)
Select values from arg[1]=threshold and down if arg[2]=0 or up if arg[2]=1
undo
Undoes as much as possible of the previous action

Display

adjustMinMax
Adjust min and max grey level values to mean ± 2 standard deviations (clipped to the volume's min and max)
colormap(name)
Colormap name is a string among {autumn, bone, winter, hot, water, solidred, solidrgb, jet, jetrgb, negpos, gray}
setMinMax(min,max)
Change the min,max values used for display to arg[1,2]=min,max
setSelectionColor(red,green,blue)
Change selection color to RGB=arg[1-3]
setSelectionOpacity(opacity)
Change selection opacity to arg[1]

Mesh commands

flipMesh(plane)
Flips the mesh (if loaded) along the dimension argv[1]=x, y or z
loadMesh(path)
Load a mesh in text format at arg[1]=path
pushMesh(distance)
Push the mesh (if loaded) by arg[1]=distance along the normal
reorientMesh(new_orientation)
Change the current 'xyz' orientation of the mesh (if loaded) to that of the string in arg[1], for example, zxy
saveMesh(path)
Save mesh (if loaded) at arg[1]=path
scaleMesh(value)
Scale mesh (if loaded) with arg[1]=scale factor
translateMesh(x,y,z)
Translate mesh (if loaded) by adding arg[1-3]=x, y and z displacements
voxeliseMesh
Voxelise mesh (if loaded)