AVS Modules confocal slicer EMBL Light Microscopy Group 12 August 1994 NAME confocal slicer - slice through a three dimensional field, with the slice plane at an arbitrary orientation. SUMMARY Name confocal slicer Type mapper Inputs field 3D uniform byte (1- to 4-vector) Outputs field 2D irregular byte geometry Parameters Name Type Default Min Max Choices X,Y,Z Rotate float 0 -360. 360 X,Y,Z Translate float 0 UNBOUNDED X,Y Scale float 1.0 UNBOUNDED U,V Mesh Resolution integer 20 10,500 Background Value float -1.0 UNBOUNDED Field Output integer 0 0 1 DESCRIPTION The confocal slicer module extracts a 2d slice from a 3d field. Output consists of a 2d field or a geometry. The position, size and resolution of the slice plane are under user control via the parameters. For all input fields, the module will determine "sane" parameter settings for extracting an initial slice. This is basically a hack from the module new_arbitrary slicer from IAC (appologies to Wes Bethel). The intention is to use it for slicing data collected from a confocal microscope. This is uniform byte data with one or more values per point in space. The advantages are: 1. support for fields of vector length 1 to 4 added. 2. support for field sizing added. The module looks at the fields->points values in the field and scales it accordingly. i.e. the output will not be distorted ! Thus, the input field MUST have: field->points[0] = minimum dimension of field in x. field->points[1] = maximum dimension of field in x. field->points[2] = minimum dimension of field in y. field->points[3] = maximum dimension of field in y. field->points[4] = minimum dimension of field in z. field->points[5] = maximum dimension of field in z. 3. output can be directly as geometry !!!! module output can thus be fed straight into the geometry viewer. This not only saves one module, but the geometry produced is more compact since a number of channels are mapped to one set of vertices and colors. (no more messing around with mutiple slices, colormaps and transparency). 4. support of types irregular and rectilinear removed. Scan mirror systems in confocal microscopes are locked to some sort of electronics which sample in a regular fashion. I cannot therefore see a use for these field types. NB. If you want to use the field output to view your slice, remember that image viewer will only display square pixels (despite having all that lovely points information). To get the proportions correct you therefore need to set the x and y scale equal, AND the Mesh resolutions equal INPUTS Data Field, 3D, uniform, byte. PARAMETERS X,Y,Z Rotate | These just control the position and orientation X,Y,Z Translate | at which the slice is taken X,Y Scale | U,V Mesh Resolution This is the number of samples taken in the two orthogonal directions on the slice. Background Value Bits of the slice which hang outside the field being sliced will be filled in with this value. Field Output This toggles output beween geometry output (default) and field output. OUTPUTS Data Field, 2D, irregular, 3-coordinate scalar float. The output field is 2D instead of 3D and is an irregular field. EXAMPLE The following network takes a slice from a field and displays it: READ FIELD |_____________________ | | CONFOCAL SLICER VOLUME BOUNDS | | | | | | | ------------------- | | IMAGE VIEWER GEOMETRY VIEWER AUTHOR Nick Salmon, Light Microscopy Group European Molecular Biology Laboratory Meyerhofstrasse 1 69117 Heidelberg Germany email: salmon@EMBL-Heidelberg.DE This is basically a modification of code from: Wes Bethel, Lawrence Berkeley Laboratory AVS Modules confocal slicer EMBL Light Microscopy Group 12 August 1994