Module: HCS Plate Manager ()

Description:

This is an experimental module from the Xtra Library: https://xtras.amira-avizo.com.

This module enables loading, visualizing and processing multi-channel fields from Thermo Scientific CellInsight CX5, CX7 LED and CX7 LZR HCA instruments and HCS Studio software. The data must be provided as a folder containing DIB files, the native image format for HCS Studio software.

Fields are loaded as MultiChannelField objects in the Amira Project View. An option is also available to load and stitch all fields from one specific well as one whole MultiChannelField object. MultiChannelField objects can be visualized in 3-dimensions with OrthoSlice, Volume Rendering, or Image Ortho Projections.

The module also allows applying a recipe to a single field, or to all fields of the plate. In the latter case, outputs of the recipe are saved in the specified output directory. All wells and fields are processed independently from each other.

Known limitations: The entire plate must be acquired with a constant number of slices and z-spatial positions for all channels of a field. Kinetic data acquisition are not supported.

Ports:

Console

Opens the Python Script Object console of the module as the active console window.

Plate Directory

Directory containing DIB files, as exported from HCS Studio software. The current module relies on the file naming conventions for wells, fields, channels and slices.

Plate Info

Indicates the number of wells, fields and channels detected in the input folder.

Mode

Select the action that will be performed when pressing Apply:

• Load individual fields as multi-channel volumes.
• Load and process an individual field using a recipe.
• Load and stitch all fields from one specific well as one whole multi-channel volume.
• Process all fields of a plate in batch using a recipe. All wells and fields are processed independently from each other.

Wells

Selects a given well.

Fields

Selects a given field from the selected well.

Recipe

Recipe to be applied to 'Process Current Field' or 'Process Plate'. For MultiChannel fields, the recipe must be able to handle MultiChannel inputs. The module 'Channel Selector' can be helpful for designing such recipes.

Output Directory

In 'Process Plate' Mode, the results from the recipe will be saved in this output directory.

Processing Field

In 'Process Plate' Mode, indicates the fields currently being processed.

Processing Time

In 'Process Plate' Mode, indicates the elapsed and estimated remaining computation time.