• Step-by-Step Analysis: Workflows provide a structured, step-by-step approach to image analysis, creating a complete Imaris scene while leaving visualization adjustments unchanged.
• Export and Import Workflows: Users can export workflows from one dataset and import them into another, ensuring seamless sharing and reproducibility.
• Workflows as Batch Protocols: Workflows can be used as simple or complex batch protocols, supporting both fully automated and manual steps. This ensures flexibility when processing multiple datasets.

Users can now use automatically or manually created Surfaces as Regions of Interest (ROIs) for subsequent detection of Spots, Surfaces, Filaments, and Cells. This functionality enables targeted analysis by limiting detection to specific regions, improving accuracy and efficiency.

Using Imaris Surfaces or Spots as masks to create channels of interest (i.e. delete signal outside of Surface or delete signal inside the Surface) has often been used by Imaris users. Since Imaris 11.0, this feature is fully integrated into Workflows and Batch processing (Image edit option), allowing users to apply automated masked channel creation across multiple datasets.

Benefits:

• Simplifies workflows by automating masked channel creation.
• Enables targeted analysis and visualization of specific regions or features.
• Increases efficiency in multi-dataset analysis.

A new Machine Learning Filter has been introduced to enhance the detection and classification of Spots and Surfaces. This feature allows users to apply advanced filtering methods based on machine learning, improving the accuracy of object identification and segmentation.

Users can now export only selected statistical values in a tabular format, making downstream analysis more efficient. This targeted export feature simplifies data handling for external statistical tools.

Workflows now support the inclusion of manual steps within Batch processing. For example:

• Users can manually edit objects (Spots, Surfaces, Filaments, Cells) in one step and then automatically track them in subsequent steps.
• During Batch runs, the user will be prompted to complete manual steps for each dataset, after which the Batch will continue to process automatically.

This feature combines the power of automation with the precision of manual adjustments.

Imaris 11.0 introduces the ability to save multiple "Views" within a dataset using Snapshots. This way researchers will always be able to save multiple interesting angles inside one dataset. Imaris also now allows to create multiple Key Frame Animations for one dataset to save time recreating visual stories.

• Snapshots are now part of the Workflow, storing Channel colors and Display Adjustment settings.
• Users can easily apply the same color schemes across multiple datasets.
• Snapshots are automatically added at the end of Batch Workflows for quick quality control, enabling fast visual inspection of results.

Imaris Cell now supports the automated import of pre-created Surfaces and Spots as part of a defined Workflow. This operation is fully batchable, streamlining the analysis process for repeated tasks.

The new options inside 1D and 2D Vantage Plots allow users to compare analysis results across experimental groups and datasets, providing powerful tools for identifying trends and differences in data.

Imaris 11 brings back the spine diameter calculation method from version 9.9, which together with the 10.0 method is offering users two options for automated spine analysis. This provides flexibility to choose the approach that best suits their data and analysis needs.