Aivia Software

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About

Aivia’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 Aivia Experiment format to save conditions, plate, alignments, and optionally convert to Aivia image format. Once an experiment, plate, well and field is identified, you can open the field into the main parts of Aivia for viewing and analysis.

Main Topics

  • Overview

  • Quick Start

  • Tips

Overview

  1. Experiment Selector - If you have multiple experiments loaded, you can change between them here.

  2. Experiment Loading - Load, Reload, and Save your experiments.

  3. Plate Settings - Set your plate and reposition the field positions.

  4. Plate Selection - When you have multiple plates/sample in your experiment, they show here.

  5. Well Explorer - Zoom/Pan and select wells. Selected wells change what is displayed to the right, as well as affect the Conditions area below.

  6. Field Explorer - Zoom/Pan and explore your fields in your wells.

  7. Conditions Editor - See and edit conditions for all wells selected in the Well Explorer.

On this page:

Quick Start

1. Capture your experiment in LASX

2. Import - Via the Load Experiment button (.xlif, .xlcf). This creates a new Aivia Experiment and puts plates into the Aivia Experiment. Usually the path of the file to load is LASX_Experiment/Metadata/Sequience.xlcf, but you can try others too.

3. Setup Plate - Set plate and offsets/alignments.

4. Select Wells - Via rows, columns, or individual wells. You can hold ctrl to multi-select.

5. Set Conditions - After selecting the wells you want to change conditions for, press the Conditions button near the bottom middle. Add or edit the condition(s) and group(s), and hit the + button to add it. Close the Edit box to see the changes. You may need to close and select a different subset of wells to complete your Condition editing.

You can select the Condition or Group to highlight the wells with that Condition or Group. The drop down below the Well Exploere selects a Condition, and highlights groups in different colors.

6. View and identify field(s) of interest - In the right side Field Explorer, zoom with mouse wheel, pan with right click drag, hover over fields, and double click on one to open it in Aivia’s main viewer.

Tips

Here we will share some ideas, tips, tricks and steps to help you get the most out of Aivia’s Experiment Explorer

Use with Workflow Processor

Remember to save your experiment if you have added/edited any well Conditions that you want to use with the Workflow Processor. In the Workflow Processor you will need to load/reload the experiment you just saved.

Overlapping Fields

In the Field Explorer (right side of Experiment Explorer), 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 Field Explorer when there are too many to display. At this time the limit is based on number of fields in selected wells (selected in the Well Explorer, middle of Experiment Explorer), 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.

Export Experiment Data

At the top right of the Experiment Explorer’s tool bar is a button that aggregates and exports all the experiment-level data. This data is gathered from individual fields that have been preprocessed, for example by the Workflow Processor. If you setup an Aggregate Results Viewer in Aivia’s options (eg. CytoMap), this button will also attempt to auto launch and import the data into it.

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