This guide explains how to create spiral based boxes.
The boxes can be used as ROIs for further analysis (Compartmentalization, gradient distribution, heat map, etcetera)
Creating spiral oriented sub volume»
Loading the Python script
- Open Python Script Editor. From the Extra menu, select Script Editor.
- Load the Free-Oriented Sub-volume Python Script.
- Browse the folder on which the file has been saved.
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.
Setting the script features
- In order to define the spiral distributed sub-regions (sampling volume) features, some 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_PLANEdefines the lower Z plane of the sub-regions ROI.LAST_PLANEdefines 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). STEP_ANGLEdefines the step size in degrees. The boxes will be positioned on the spiral curve everySTEP_ANGLE.SPIRAL_LOOPdefines the number of loops (concentric spirals). Any single loop is a complete 360° spiral. Values less than 1.0 draw a partial spiral.COEFFICENT_Bis the coefficient used to define the distance between the loops of the concentric spiral.BOX_HEIGHTsets the height of the boxes (Y).BOX_WIDTHsets the width of the boxes (X).
Both are expressed in pixels.
Set the distance of the loops and their numbers according to the size of the boxes. Wrong parameters setting can make the boxes overlap, especially inside the inner part of the spiral.
Running the Python script
Run the Spiral 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.
Viewing the results
- Results (segments and measurements) will be stored in the dataset only if the Store Objects operator has been correctly set. Tick appropriately the option as shown below before complete the pipeline execution.
- Open the data table if not already visible.
- Measurements are now visible in the data table.
Note: The spots count in the single sub-region is shown in the data table. The empty sub-regions are not listed. To get the total spots count the group statistic feature must be used.
Features can be added or removed from the data table using the Feature Column command.