In the ID7000 system software, users can create experiments from a template, an existing experiment, a single-stained sample, or a multicolor assay to accommodate their preferred approaches. New users can create new experiments with the Experiment Design Wizard. To accommodate multi-sample and multiparameter experiment needs, the ID7000 software provides both a Shared Worksheet and an Individual Worksheet. A Shared Worksheet allows each sample in a group to use the same worksheet and thus makes experiment setup more intuitive.

Instrument settings can be specified for each sample group and configured for lasers and detectors to give researchers the needed flexibility. Altering these settings for a sample in a group changes the settings for all unmeasured samples belonging to the same group. Instrument settings can be exported and imported
as needed.

The acquisition functions are all accessible from the Acquisition tab and have been developed keeping a multi-laser workflow in mind. The tab accesses all functions that control the data acquisition, recording, and stopping, as appropriate, while monitoring the data acquisition status. To enable walkaway functionality, the system has an Event Checking function that can be set to stop or skip and continue automatic acquisition if the event rate drops or air bubbles are detected.

For sample analysis, the appropriate spectral references must be selected and fluorescence unmixing applied to remove the spillover components from each fluorescence channel. The unmixing can be manually adjusted on the screen using the Spectral Reference Adjuster. Making changes on one plot will result in the changes being applied automatically to all other plots having that fluorochrome as one of their parameters. Users can save the adjustment result as a new fluorescence unmixing matrix or can overwrite an existing fluorescence unmixing matrix.

The Analysis tab houses all controls for analysis operations on the ID7000 spectral flow cytometer, providing access to worksheet tools that let users choose how the data is displayed (such as plot types), and customize the display for their analysis needs. Plots and statistics provide real-time information during acquisition. The Experiment Explorer pane allows search by date and keyword, to display desired data on the worksheet. Once displayed, plots can be edited individually or as a group, to facilitate working with complex gating hierarchies.

The software also supports batch processes for users who need to run multiple samples, for operations like experiment setup, data acquisition and analysis, and export of data and statistics. Combined with the ability to program an automated shutdown, this enables scientists to focus on discovery instead of repetitive tasks.