Editor

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Workflow Processor - Editor Tab

The Editor is where most of the settings are picked. This is where parts of Aivia are able to be chained together. Once you are done, save the .workflow file with the Save icon on the right side and you can use those settings over and over.

Legacy Workflow Editing can still be performed on any old workflow file or through the advanced menu in the Create New Workflow button.

Workflow Creation

There are two primary paths to creating workflows.

• Automatic creation through the Batch Workflow Creator tool (Recommended)

• Advanced Manual Creation from the “Create New Workflow” button

Advanced Manual Creation

Clicking the “Create New Workflow” button will create a blank slate to generate a workflow from. A single processing step for the purposes of loading an image will by default be added. Processing is done from top to bottom in sequence, to add a new processing step to the workflow, click the “Add Processing Step” button. The trash can button allows removal of processing steps. The arrow buttons allow reordering the steps.

Processing Steps

There are many different types of processing steps that a workflow can perform. The general premise of a workflow is to Load an image, process the image, and then save the results. Mixing and matching different processing steps allows a powerful combination of capabilities.

Loading

• Image Load

  • Loads a single file defined in the “Runner” tab

• Image Sequence Load

  • Loads a sequence of files into a single file with automatic identification of the format

Processing

• Object Classifier Apply

• Pixel Classifier Apply

• Recipe Apply

  • Preset Measurements are considered Recipes for the purposes of workflows

• Image Enhancement Apply

• Segment By Example Apply

• Spatial Relations Apply

Additional

• Save Data

  • This step is generally not needed except for in advanced use cases, such as saving intermediate data. The Runner step will handle saving data based on the selection in its UI. Adding a save data step will save independently of the Runner’s settings

Expanding the Options section of a processing step will allow modification of the parameters of that step.

Custom Measurements

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Measurement Preset tool from the Analysis Menu

This is an optional, and advanced step. Most users will be happy using the measurements that Recipes include. In case you have specific measurements you want to include, you can save your measurements in the Analysis menu, Measurement Preset Tool. Once you have a Preset in the Measurement Preset Tool (either create or load one), you can select that preset in the Workflow in the Custom Measurements, Recipe area. To add custom measurements use the “Recipe Apply” processing type and the Preset Measurement recipes loaded in the Measurement Preset Tool will be available for selection.

Also see the Input Selections below.

Warning: Custom Measurements can be confusing and only recommended for highly advanced users.

Input Selections

Each processing step can have one or more Input Selections, depending on what you have selected. It is here that you describe to the workflow how you want your images to be processed. There are cases where we are unable to know what is desired. For example, the images you are going to process already have results, or will have more/less channels than the one you did your analysis on. Since Aivia has not opened or seen these images, it cannot guess what is desired.

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Knowing the format of the input files as well as the required inputs to the processing steps is important in selecting the right values. When automatically created leaving the input selections at their default will yield the results you are looking for. Other times you may have to adjust some Channel or Object Set Inputs. The input sector defines which channel is used by the step. If your image was loaded with 2 channels, and the previous step creates a 3rd that you want to use in this step, choose 3.

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New Classification is the 3rd index in the list of object groups

For the purposes of selecting Object Sets/Groups the index is based on any hierarchy being flattened. For example, “New Classification” is the 3rd index in the picture provided.

Warnings:

• Some recipes have a large number of input selectors, please try on a example image to ensure you have the settings right.

• It is recommended to not adjust any Object Set inputs unless you are an expert.

• Beginners are recommended to use the Automatically Create Workflow method.

Runner

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Workflow Processor - Runner Tab

The runner is where you run workflows. You can load previously created workflows, or select one you have just created. There is an Edit icon on each available workflow which will take you to the Editor.

File Input

Select your files, folders full of files (includes all children in subfolders too), or Aivia Experiment file (see the Experiment Editor [todo: add link]). Any file that Aivia can normally open is processable here. Library files will load all the files and you can filter by removing fields you don’t want. Aivia Experiment files will give you an option of filtering by Conditions that were previously setup in the experiment.

Note: If the workflow had its Image Format set as Single from Many, all selected images will be stacked together into a single image, and you will get one set of results.

Saving

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Workflow Runner - Save options

Here you can choose what and where you want your things.

Warning: The Save Folder should be a place with lots of space, and ideally with not too long of a path name. Windows has a 256 character limit, and Workflows will output some folders and files with longer names (assuming you have long-named workflows and files). If the save folder + folder structure that workflows make + file names are beyond that limit, the job will fail and you will need to make some changes before running again. There is a rumor of a setting in Windows that allows longer paths, but we have not seen that work. Each time you start a workflow it makes a subfolder in the Save Folder with the date and subfolders in that folder for each image/job. Experiments add some additional folders to keep everything organized.

Additional Save Options: Make sure you choose Save Field if you want to save an Aivia.tif with all the objects/measurements on it.

• Save Field - Save the processed image, detected objects and measurements to a single Aivia.tif.

• Export Measurements to .xlsx - Export in Excel format

• Export Measurements to .csv - Export in comma-separated format

• Export Channels - Each channel in the processed image will be saved to a separate tif file

• Export Objects as Masks - Each object set in the processed image will be saved to a labeled tif

Queue

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The Queue displays jobs that have yet to start, as well as the currently processing job, along with its status. You can hit Pause to hold the queue. The next job won’t start, but the current job will complete.

You can resort the queue by pressing the Up / Down arrows next to each job, or remove a job by pressing the delete button. There is a Clear Queue button at the bottom that will remove all queued jobs.

History

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The History panel shows all the jobs that have completed (or failed). Restarting Aivia will clear the History, or you can push Clear All at the bottom of the history list.

Clicking on an item in the history list will show some details and even a preview if possible. Previews list the centers of all detected objects (if any) with pink dots.

Each Item has some details, and a few buttons:

• Save: Saves off a .json file of details about the objects detected.

• Open: Opens a Windows File Explorer to that file’s location on disk.

• Delete: Removes that history item from the list.

The bottom of the History list has a Clear All button that you can use to remove all history items.

Lastly, in case of any error, the history item will have a red border, and clicking on it will tell some details about what happened. Please check Aivia’s log (Aivia > File > Options > Logging) for more details.