This guide explains how to create a sampling volume (ROI) as a XYZ matrix of boxes. The application uses a Python script to create single or contiguous sub-regions that can be used as ROI for further analysis. The unique limit is related to the sampling volume shape. Only regular 3D boxes are available.
Creating XYZ matrix of sub-volumes
Setting the script features
In order 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.
Only the parameters located in the USER SETTING area can be modified. Don’t change any other number, definition or text in the code outside this dedicated area.
SIZE_BOX_X= the X axis size of each box . The value is expressed in µm.SIZE_BOX_Y= the Y axis size of each box . The value is expressed in µm.SIZE_BOX_Z= the Z axis size of each box . The value is expressed in µm.
PRESERVE_EDGES= This option sets the boxes touching / non touching feature. IfTRUE, the boxes edges are not contiguous to each other (2 pixels space in between).
Note: The volume sizes (XYZ) are divided by the single box XYZ size. The integer number of boxes fitting in the volume is computed. It may happen that the boxes don't cover the whole sample volume.
TAG_SEGMENTS= defines the segments TAG to be used to compute the boxes. It is used as alternative of the standard method (whole volume). If empty, the default method (whole volume) is used.TAG_BOXES= defines the TAG assigned to the created boxes.TAG_SEGMENTS = “”TAG_SEGMENTS = “Manual”
Note: If theTAG_SEGMENTSis set to an existing TAG, all the objects belonging to it are used to create the boxes matrix. Specifically, the bounding box volume of each object is taken as the reference volume that is divided into boxes.
Running the Python script
Run the Free-Oriented Sub-volume Python Script by pressing the Run Script button or pressing the F5 key.
Note: Activate the Output Panel, if not already displayed. The status of the script execution (errors including) will be visualized here.