Batch Workflow Creator

The Batch Workflow Creator refers to the button towards the top of Aivia 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, “New Classification (test)” and “Nuclear Membranes” were selected (Green Area)

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In this case 3 “steps” were identified:

1. Two different channels were loaded from disk

2. A recipe was applied using the previous channels

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

   1. Note that the Object Classifier used measurements which required a channel input

Because “New Classification (test)” and “Nuclear Membranes” were selected, those steps are 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. Depending on how the window was opened, if from the “Batch” button it will then present the Workflow Processor with the workflow loaded to begin batch processing. Alternatively, if from the Experiment Explorer’s Cog Wheel icon, the workflow will be loaded into the selected workflow for the purpose of Assay Apply.

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 Measurements (Blue Area)

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 measurements for the Object Sets/Subsets that which are involved in the operations into an included step in the generated workflow. This is useful in the case of having existing data on the image and the workflow to be created is adding additional analysis.

Save Individual Components (Blue Area)

This checkbox is available when generating workflows from experiment related data. When selected, this operation will automatically save every component of the generated workflow into a folder alongside the experiment file currently active. If the experiment file does not have an on disk location, a prompt will appear requesting a desired save location for the workflow components.

Operations Graph (Brown Area)

Operations which will be involved in the creation of the workflow appear in this area. The operation boxes may be moved by clicking and dragging, this may be useful in graphs in which many operations appear.

A screenshot may be taken of the currently display graph by clicking on the (Screenshot button) in the Orange Area near the top right corner of the graph. To reset the graph to its original layout there is also the (Reset button) in the same area.

Tooltips

Hovering over the items in the Workflow Creator will display information about that item. In this case, the tooltip for the Object Classifier indicates the “test” Object Classifier’s location on disk, that takes in the Object input from the Object Set named “Cell Membranes” and a Channel named “405_mBlue” for measurement purposes.

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The red lines can also be hovered to show exactly which inputs are assigned to what operations.

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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