Python Scripting in Amira & Avizo Software | 3D Image Analysis & Workflow Automation

Accelerate image analysis with automated workflows, custom tools, and integrated Python

Thermo Scientific Amira Software for life sciences and Avizo Software for materials science, renowned for powerful 3D visualization and analysis capabilities, become even more versatile and tailored to your speciﬁc needs with Python scripting. By integrating Python 3, Amira and Avizo Software allow users to leverage a wide array of scientiﬁc and analytical packages, including NumPy, SciPy, Matplotlib, PyQt, OpenCV, Keras, PyTorch, and scikit-learn.

Enhanced data processing with Python 3

NumPy delivers eﬃcient multi-dimensional array handling, simplifying complex mathematical operations on large datasets.

SciPy can be used for advanced scientiﬁc computations, such as interpolation, integration, and optimization, to reﬁne your data analysis processes and perform sophisticated image processing tasks, including ﬁltering, transformation, and feature extraction, to gain deeper insights from your data.

Build custom scientific visualization and GUI tools with PyQt and Matplotlib

Matplotlib offers interactive plotting and visualization, allowing you to present your data clearly and intuitively.

PyQT allows you to develop your own graphical user interfaces (GUIs) to enhance user interaction and streamline workﬂows, making the software more tailored and eﬃcient for speciﬁc tasks.

Flexible python environment management for reproducible workflows

Create multiple self-contained Python environments with their own packages within Amira and Avizo Software, ensuring compatibility and isolation for diﬀerent projects.

Manage dependencies and package versions easily, preventing conﬂicts and ensuring that your scripts run smoothly across various projects and collaborations.

Seamless Python integration

Enjoy the same performance and memory eﬃciency as standalone Python applications thanks to Amira and Avizo Software's tight integration with Python.

Execute Python scripts directly within the software environment, allowing for simple data exchange and interaction between Amira or Avizo Software and your custom Python code.

Elevate your workflow with Python by interacting directly with modules and adjusting their properties in real time. Turn complex module configuration into simple, repeatable automation that accelerates delivery and boosts developer productivity.

See Avizo Software with Python scripting in action

CellPose segmentation

Use pre-trained CellPose models to predict instance-level segmentation and labeling in both 2D and 3D data, applicable to a variety of generalized objects.

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kMeans clustering on label analysis

This Xtra implements kMeans clustering on a label analysis spreadsheet. Separated objects can be clustered based on any built-in or user-customized measure group.

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