Batch Workflow Creator

Aivia Software

Batch Workflow Creator

The Batch Workflow Creator refers to the button towards the top of Aivia Untitled-20250314-213309.png which allows the user to access a drop-down of options for automatically creating workflows from data on the active image in Aivia. This system can create a workflow from 3 primary sources of data; Channels, Objects, and Spatial Relations. To automatically generate workflows the data must have been created in Aivia 15 or newer. Data generated prior to Aivia 15 may not have the historical records to ensure proper generation.

General UI

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The Batch button to start this process can be found near the top of Aivia next to the Guided Sequence Chevrons.

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Once clicked the button will present options to generate the workflow from. Note that options which do not have compatible data will not appear.

  • Objects

    • Object Set

      • Data generated from processing steps like Recipe Apply, Segment By Example, etc

    • Object Subsets

      • Data generated from Object Classifier(s)

    • Manually generated objects

      • Editing, Gating, and similar operations will not display in this menu since there is no automated way of replicating that action

  • Channels

    • Data generated from general “Preprocessing” steps like the Pixel Classifier or Image Enhancement Tool

    • Channel Images not generated in Aivia will not be available to select since there are no steps in Aivia to reproduce them with

  • Relations

    • Data generated from generally the Spatial Relations tool which defines relationships between two sets of Objects

 

Selecting an Item

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Because objects have multiple layers there may be a cascading set of objects to select from. Any of these items are select-able to generate from.

  • Selecting “Cells” in this case will produce a workflow with the Cell Count Recipe as the primary processing action

  • Selecting “My Object Classifier” or either of the children (“New Classification” and “New Classification (1)”) will produce a workflow with Cell Count AND Object Classification

Once an item is selected Aivia will prompt the user with the information which will be used to create the workflow.

Workflow Creator

In the below example, “My Object Classifier” was selected.

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In this case 3 “steps” were identified:

  1. A channel was loaded from disk

  2. A recipe was applied using the previous channel

  3. The objects generated from that recipe were then classified using the Object Classifier

Because “My Object Classifier” was selected, this step is highlighted in yellow/gold, indicating it to be the desired output.

Create Workflow

Clicking “Create Workflow” will prompt for a place to save the workflow, it will then present the Workflow Processor with the workflow loaded to begin batch processing.

Note that because of the diversity of data that can exist, the Workflow system generally uses Index matching to process data. This generally works perfectly IF the data to be batched on matches the exact state of the image which the workflow is generated from. The processing steps generally will find what the index of the input/output was and use that as the parameter for the workflow to process each step individually. If the image the workflow is generated on does not or will not match the data to batch on, editing of the workflow may be required to align them.

Include All Field Measurements

Because recipes, classifiers, etc dictate their own measurements, it is reasonable that measurements may have been added post Recipe Apply, Segment By Example, etc., because of this the option to include all of the active measurements is possible. This checkbox allows the user to include ALL measurements that are on the active image into an included step in the generated workflow. Note that by ALL that includes any measurements not directly relating to the displayed information. This is useful in the case of having existing data on the image and the workflow to be created is adding additional analysis. However, this can cause issues if measurements from data that exist on the current active image do not exist on the batched images this created workflow applies to in the future.

Tooltips

Hovering over the items in the Workflow Creator will display information about that item. In this case, the tooltip for the Cell Count recipe indicates that Cell Count takes in the Channel Input from the recipe named “Input Image” and outputs an object set named “Cells”.

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The red lines can also be hovered to show exactly which inputs are moving where.

Detailed information

If more detailed information is required, all data related to the generation of workflows can be found in the Action History or Event History tools which are found in the “View” menu item.

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