ZEISS Knowledge Base

Creating concentric sub volume - matryoshka dolls

This guide explains how to create concentric objects based on the source segments shape, from the outside to the inside. The concentric shapes can be used as ROIs for further analysis (Compartmentalization, gradient distribution, heat map, etc.).

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 Matryoshka_doll_revxx Python Script.
Browse the folder on which the file has been saved.

Python script code usage rights:The user has the permission to use, modify and distribute this code, as long as this copyright notice remains part of the code itself: Copyright(c) 2021 arivis AG, Germany. All Rights Reserved.

Setting the script features

In order to define the "Matryoshka" based model sub-regions 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.

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.

TAG_DESCRIPTOR : Set the source object(s) TAG. The outer shape of this/these object(s) is used to create the concentric, inner, sub-volumes.
TAG_SCRIPT_DESCRIPTOR : It defines the new TAG with which the concentric objects will be identified. The source object ID is added to the TAG.
MATRYOSHKA_DOLL_NUM : Sets the total number of concentric sub-volumes. The parameter includes the outer source shape.
APPLY_CONVEX_HULL : If True, the convex hull algorithm is applied.
MATRYOSHKA_WITH_HOLES : If True, the inner sub-volume is subtracted from the outer contiguous shape.

The MATRYOSHKA_WITH_HOLES parameter changes with how the inner sub-volume of each Doll is computed. It can be hollow or filled.

MATRYOSHKA_WITH_HOLES = True