This guide explains how to create a sampling volume (ROI) freely oriented along X and Y axis.
The application uses a Python script to create single or contiguous sub-regions that can be used as ROI for further analysis.
Creating freely XY oriented sub volumes
Drawing the reference ROI
- Switch the Viewing area from 4D to 2D view mode.
- Select the Draw Objects tool.
- Select the Brush tool.
- Draw the 2D ROI over any Z plane. Use the Erase Brush to correct the ROI if necessary.
- Press the green icon to confirm the ROI.
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Setting the script features
To define the contiguous sub-regions (sampling volume) features, few parameters of the script should be adjusted to match your analysis needs. These parameters are located in the code area labeled as USER SETTING.
- Set the Z planes range.
FIRST_PLANE defines the lower Z plane of the sub-regions ROI.
LAST_PLANE defines the higher Z plane of the sub-regions ROI.
The values of -1 set the Z planes range equal to the whole volume depth (total number of Z Planes available). - COMPUTE_MAIN_BOX = True enables the creation of an additional ROI having the same sizes of the total subregions ROI size.
- NUM_BOX_LENGHT defines the number of sub-regions along the main axis (the longest one). NUM_BOX_WIDTH defines the number of sub-regions along the minor axis (the shortest one).
Note: Set the number of sub-regions accordingly to the total size of the reference ROI. Don’t create boxes too small.
Examples:
NUM_BOX_LENGHT = 10
NUM_BOX_WIDTH = 1
NUM_BOX_LENGHT = 10
NUM_BOX_WIDTH = 2 SIZE_IN_VOXELSdefines if the size of the Sub-Volume is expressed in metric unit (True) or it is calculated from the reference ROI size (False).SIZE_BOX_HORandSIZE_BOX_VERdefines the Sub-Volume XY size in microns. The sizes are referred to a single box.SIZE_IN_VOXELSmust beTrueto create the box in microns.
Note:NUM_BOX_LENGHTandNUM_BOX_WIDTHare also involved in the metric Sub- Volume creation.
Examples:SIZE_IN_VOXELS = TrueNUM_BOX_LENGHT = 1NUM_BOX_WIDTH = 1SIZE_BOX_HOR = 10 (microns)SIZE_BOX_VER = 30 (microns)SIZE_IN_VOXELS = TrueNUM_BOX_LENGHT = 3NUM_BOX_WIDTH = 2SIZE_BOX_HOR = 5 (microns)SIZE_BOX_VER = 10 (microns)