Aivia Software
Experiment Explorer
AboutAivia’s Experiment Explorer is primarily for viewing and navigating multi-field/multi-image well plate experiments acquired with LASX (.xlif, .xlcf). Once opened in Aivia’s Experiment Explorer you can save the experiment into the Aivia Experiment format to save conditions, plate, alignments, and convert to Aivia’s image format. Once an experiment, plate, well and field is identified, you can open the field into the main parts of Aivia for viewing. |
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Overview
Experiment Explorer Toolbar - Select your experiment, Load, Reload, and Save your experiments, etc.
Plate View- Zoom/Pan and select wells. Selected wells change what is displayed in the Well View.
Well View- Zoom/Pan and explore your fields in the wells selected in the Plate View.
Conditions Editor - See and edit conditions for wells in the Plate View.
Assay Apply - Apply assays to wells.
Measurements - View aggregated measurements for wells that have had an assay applied to them.
General Workflow
Load an Aivia experiment file or a LASX file (1)
Set metadata like conditions in the “Conditions” tab (3)
Apply an assay in the “Assay Apply” tab (4)
Review results in the “Measurements” tab (5)
On this page:
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Experiment Explorer Toolbar
Import - Via the Load Experiment button (.xlif, .xlcf, .lif). This creates a new Aivia Experiment and puts plates into an Aivia Experiment. Usually the path of the file to load is LASX_Experiment/Metadata/Sequience.xlcf, but you can try others too. You can also open from an existing Aivia Experiment file.
Name | Look | Description |
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Experiment selector/dropdown |
| Let’s you select the plate/experiment to view in the Experiment Explorer. You can close individual experiments by clicking the trash can icon. |
Clear current experiment |
| Closes the currently viewed experiment. |
Clear all experiments |
| Closes all loaded experiments. |
Clear selected experiment’s data |
| Removes all the measurement and object data from the selected experiment. |
Load Experiment |
| Load either an existing Aivia experiment (.experiment) or an LASX file (.xlif, .xlcf). Loading an LASX file creates a new Aivia Experiment and puts the plate into it. Usually the path of the file to load is LASX_Experiment/Metadata/Sequience.xlcf, but you can try others too. |
Reload Experiment |
| Reloads the currently selected experiment. |
Save/Save As |
| Saves the experiment in place or elsewhere, copying all the image data to the new location. Clicking “Save As” will open a “Save Experiment” dialog that lets you pick the location and the name of the experiment folder/file. |
Copy Conditions Format |
| Copies the currently selected plate setup (unless it’s provided by LASX metadata), and the condition assignments for wells. See also the Paste Conditions Format button. |
Paste Conditions Format |
| Pastes the last copied plate setup/offset and the condition assignments for wells. |
Export Measurements |
| Opens the measurement export dialog. See the “Measurement” section for more info. |
Select & Adjust Plate |
| Opens the plate selection and adjustment dialog. You can adjust the xy offset of all the FOVs in the image by dragging the blue box, or by using the adjustment up downs. You can also select a plate, if your image metadata did not provide one. |
Plate View
Zoom with mouse wheel, pan with right-click drag, hover over fields, and click to select. The background color shows selection, the border color shows the condition group color for the currently selected condition, and the fill color shows the currently selected measurement’s heatmap color (if one is selected).
Actions:
Click to select a single well.
Click drag to draw a selection box which will select everything in the box.
Hold ctrl to add to selection, or to toggle selection.
Click the headers (e.g. A, 1, B, 2) to select that row or column, click the top left to select everything.
Select when assigning a condition group to set it for the well.
Selected wells show up in greater detail in the Well View.
FOV Filtering
You can filter the FOVs viewable in the Well View and what FOVs assays are applied to using the filtering dropdown. The top level is the acquisition group, and the lower level is the algorithm tag applied to the fields. It will only show tags that are relevant to the current data set.
Heatmap
Whatever measurement and aggregate type is selected in the measurement panel will be shown as the fill color for the wells. You can change the coloring by clicking the “Coloring” dropdown.
Well View
The Well View will display whatever wells are selected in the Plate View. Navigate and identify field(s) of interest. Zoom with mouse wheel, pan with right-click drag, hover over fields, and click on one to open it in Aivia’s main viewer. If multiple fields overlap, a single left click will open a dropdown with all the fields that intersect your click.
Conditions Editor
Add or edit the condition(s) and group(s). Hit the “+” button to add a new condition or to add a new group to the condition. As an example, you might create a condition “Dosage”, and the groups could be the dosage percentages. You can either select wells, then click “Assign” to assign them to a condition or click “Assign,” then click wells to assign them. If you hold shift, then when assigning by clicking it won’t exit the assignment mode and you can click again.
Assay Apply Panel
The Assay Apply Panel is where analysis for an entire experiment can be controlled.
Workflow
Workflows are units of processing in Aivia, they are primarily used when “Batching” data for analysis on multiple images.
Workflow Selection
Workflows available to apply to the experiment are displayed in a drop-down. The selected workflow will be the processing applied to the experiment when “Start Processing” is selected. The workflows displayed here populate from the Workflow Processor’s loaded workflow list, for any advanced operations related to workflow please refer to that page. The Workflow Processor is accessible through the Analysis menu at the top of the software.
Creating a Workflow Automatically
In the Assay Apply Panel there are two ways to create workflows. Both will generate a workflow from the image populated into the viewer. All Measurements on the active image will be included (with the “Include Measurements” checkbox,) as such, ensure any desired measurement is selected on the image prior to workflow creation and processing.
Create Workflow from Active Image Button
This button will create a workflow matching the processing used to create the currently generated data on the active image displayed in the viewer. Pressing this button will automatically generate a workflow, save all analysis steps local to the experiment file, load the workflow and select it as the active workflow all in one press.
This button is a streamlined version of what the “Cog” button does will all tree items selected without having to click through extra dialogs. It is ideal to use when the processing on the active image in the viewer contains strictly the operations wanted to batch.
Create Workflow “Cog” Button
This button allows the flexibility of the previous button but with the manual choice of a more narrow selection of the analysis on the active image. Pressing this button will take you to the Batch Workflow Creator Tool (see tool page for more detailed information.)
Selecting an item in the right panel tree will populate the processing steps used to generate that analysis action. “Create Workflow” will generate the workflow and automatically select the newly created data as the Workflow to apply in the Assay Apply Panel.
Apply To
This area describes how the analysis should work on the data in the experiment.
“Selected Wells” will apply the workflow strictly to the wells selected in the Plate Viewer.
“Plate” will apply the selected workflow to the entire Plate displayed.
Apply Groups
Apply Groups organize analysis data into buckets. Those buckets allow aggregation of the measurements from the analysis inside of it. Only similar analysis should exist in a given Apply Group, in the case of wanting to apply a different Workflow on the experiment, create a new Apply Group to place that data in. If data has been deleted from the experiment it is recommended to also create a new (or delete the old) apply group.
A new Apply Group can be made using the + icon, the pencil for renaming and the trash can for removal of a group.
Apply Groups provide the ability to tag processing with information through “Apply Group Info.” History of apply steps that have occurred is also available through the “View Apply Group History” button.
To see specific apply information about a given entry, use the Action/Event history tool on one of the processed images.
Processing/Applying
To begin processing a workflow on a experiment press the “Start Processing” button once all settings have been adjusted to match the desired outcome.
In the common case it is recommended to leave the “Clear existing data before processing” option on. Existing data on an image could cause the analysis to offset the input of an analysis step. The checkbox is available for the situation in which it is intended that data exists on the image and the processing takes that into account.
Recalculate Measurements
In the situation in which an experiment requires modification (condition editing, etc) after processing has already occurred, there is an option to fully recalculate measurements.
Measurements Panel
The measurements panel in the Experiment Explorer allows viewing aggregation measurement data produced by data from the Assay Apply Panel.
Experiment Explorer Measurement Selector
This drop-down panel allows selection of the measurements that are displayed by the software.
Apply Group
Allows selection of which “bucket” of data to populate the rest of the drop down from. See the Apply Group section for more information.
Objects
Allows selection of which analysis generated objects to display.
Measurement
Selection of an aggregation type and a measurement which is populated from the “Objects” selector.
Available Aggregation Types:
Total, Mean, Min, Max, Median, Standard Deviation
The measurements that are available are based on what the Workflow/Analysis generated. Ensure the desired measurements exist on the image prior to workflow creation.
Condition
Aggregation of measurements are performed per Condition/Condition Group, selecting a condition allows display of that condition and subsequent condition groups.
View Level
It is possible to view the measurement data aggregated at different “levels” each level providing a different view into the data.
Plate
Aggregates data up to the level of the Plate
Well
Aggregates data up to the level of Wells
Object Set
Displays the per object set data (Requires an Object Set to be selected in the “Objects” selector)
Object Subset
Displays the per Object Subset data (Requires a Subset to be selected in the “Objects” selector)
Selecting an Object Subset Group allows displaying of that groups children at the same time.
Special Experiment Measurements
All Count
This measurement provides the count of all objects considered contained by the given object row.
While in development, for time lapse data this means the result of this measurement is all time frames combined into a single number.
Subset Count/Total Ratio
This measurement displays the proportional count that the given subset contributes to it’s parent.
Subset Count / Parent Count.
This measurement is only available for subsets.
Time Lapse Support
Time Lapse is currently under development, while it is currently possible to analyze data containing time lapse information, display of that data is a work in progress. To see measurement values from different time frames the spreadsheet will synchronize with the active image displayed.
Exporting
To export measurements, click the “Export Measurements” button in the toolbar. In it, you can choose to export the raw data, or summary data for an apply group. The experiment level determines at what level to aggregate data for the summary export. Raw data is useful if you want to do custom views of the data and you want ultimate flexibility. Summary data is useful if you want to view summary data in something like an Excel chart. There are 3 supported export levels, Plate, Well, and Object Set. It will aggregate at the selected level.
Both exports will export subsets. Items will be exported with their condition and group, and each condition and group will be assigned a number.
Tips
Here are some ideas, tips, tricks and steps to help you get the most out of Aivia’s Experiment Explorer
Overlapping Fields
In the Well View, fields can be on top / under each other. Left-click once where they are all piled up to bring up a list of fields under your mouse so you can select which to display in Aivia’s main viewer area.
Too Many Fields
The Field Explorer (right side of Experiment Explorer), by default only displays up to 100 fields at a time. This is a performance consideration. You can adjust the setting (search for Experiment Explorer in Aivia’s options), but by default only the first 100 fields will be shown. A warning message appears under the Well View when there are too many to display. At this time the limit is based on number of fields in selected wells (selected in the Plate View, not dynamically based on visible fields in the Field Explorer.
Drag n' Drop
Only works with Aivia Experiment Files. Please use the Experiment Load button for LASX experiments. Single images or library style images when drag n' dropped will open into Aivia’s Image Explorer.