12 Feb 2021

High Content Screening Plate Manager

Load, visualize and process multi-channel fields from Thermo Scientific CellInsight CX5, CX7 LED and CX7 LZR HCA instruments and HCS Studio software.


This Xtra proposes a module to browse High Content Screening data provided as a folder containing DIB Files, the native image format for HCS Studio Software.

The module recognizes the plates and fields present in the folder, and allows loading individual fields as multi-channel volumes for 3D visualization in Amira, as well as processing them in batch using recipes. All fields are processed independently from each other.

The Xtra also proposes additional modules enabling the generation of multichannel recipes (ChannelSelector module), and applying a recipe to a list of files (BatchApply_RecipePlayer module).

A small example datasets containing 2 fields is proposed in the archive, as well as 2 simple recipes which will help you design your own.

To get started, set the AMIRA_LOCAL environment variable to the 'local' folder from the archive, open Amira, right-click in the Project View and create the 'HCS Plate Manager' module.