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»
Opening the working dataset
- Select Open... from the file menu.
- Select the dataset from the file browser.
The dataset is a multi dimensional, discrete, representation of your real sample volume. It can be structured as a Z series of planes (Optical sectioning) of multiple channels (dyes) in a temporal sequence of time points (located in several spatial positions).
Usually, the dataset shows a single experimental situation (a complete experiment can be composed by several datasets). The datasets are available as graphic files saved in plenty of file formats (standard formats as well as proprietary formats).
Note: The dataset is visualized according to the current rendering setting parameters. Refer to the arivis Pro Help for more details.
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.