Event details

Workshop to automate flow cytometry gating

cytométrie

A workshop "CNN workflow to automate flow cytometry gating" is organized over 2 half-days between June 20 and 24, 2022, either face-to-face, at the Endoume Marine Station, or through remote access. The participants will learn how to use the workflow developed at the MIO: perform automatic classification, evaluate the quality of the gating, send the results to a distant database (in FAIR format).

[Translate to English:] Workshop Convolutional Neural Networks to automate flow cytometry gating

Context

  • Manual gating of flow cytometric datafiles is time-consuming and may be error-prone, especially when the number of acquisitions becomes high.
  • Using supervised machine learning methods trained on data validated by several experts is a way to automate this process.
  • This workshop will present an automated workflow based on Convolutional Neural Networks (CNNs) as introduced in Fuchs et al. (2022, published in Limnology & Oceanography: Methods, DOI : 10.1002/lom3.10493
  • This workflow enables the automation of the manual gating process and the assessment of the prediction quality through dashboards and metrics.
  • It takes raw CytoSense datafiles as inputs and returns the associated abundances of six phytoplankton functional groups.
  • When validated by the user, the automatic results are sent as datasets to the ERDDAP data management platform

Aim of the workshop

The participants will learn how to use the workflow developed at the MIO: perform automatic classification, evaluate the quality of the gating, send the results to a distant
database (in FAIR format).

Practical information

  • The workshop is available in remote access (a Zoom link will soon be sent to the participants)
  • The participants who wish to attend in person could follow the workshop at the Station Marine d'Endoume CNRS, Chemin de la batterie des lions, Bâtiment 4, 13007 Marseille.
  • It will take place on two half-days during the week beginning on Monday June 20, and ending on Friday June 24, 2022 on the dates that suit the majority of people.
  • Please fill the following form with your availabilities before June 10, 2022: https://doodle.com/meeting/participate/id/dwpQj9Je
  • Installation and technical prerequisites for the workshop will soon be sent to the participants.

 

Further information

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