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. 2024 Jul 17;15:1425488. doi: 10.3389/fimmu.2024.1425488

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Copyright © 2024 Coppard, Szep, Georgieva, Howlett, Jarvis, Rainbow, Suchanek, Needham, Mousa, Menon, Feyertag, Mahbubani, Saeb-Parsy and Jones

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Overview of FlowAtlas workflow with FlowJo. Step 1: Removal of anomalous events using FlowJo plugins. Step 2: Compensation and export of new clean FCS files. Step 3: Batch correction (if required). Steps 4-6: Workspace preparation in FlowJo including resolution of channel naming discrepancies, bi-exponential transformation of all parameters and gating user-defined populations, and sample grouping. Step 7: Importing the workspace into FlowAtlas triggers automatic panel merge, embedding calculation and launches the interactive web interface. Embedded events can be re-coloured and filtered by conditions and groups defined in Step 6. ROIs can be drawn in the embedding, generating violin plots of marker expression. Box plots can be generated to show frequencies of selected populations and conditions. Novel populations identified in FlowAtlas can be validated and annotated in FlowJo. The updated workspace file can then be re-opened in FlowAtlas to import the new annotations. FJ, FlowJo. FA, FlowAtlas.