Channels and Slots

ImageC distinguish between two types of pipeline elements: Channels and Slots. Both can be added in ImageC’s overview panel. ImageC is actually limited to a maximum of 10 channels and 6 slots.

Note

In the course of an analysis, the channels are subjected to processing prior to the slots.

The processing order of channels and slots is defined as following:

1. Reference Spot channels

2. Spot, Nucleus, Cell and Background channels in parallel

3. Voronoi slot channels

4. Intersection slot channel

OME channel information at the right-hand side

Channels

Image channels

An image may comprise one or more C (channels), with each channel in turn consisting of a series of T (time) stacks, and these in turn consisting of a series of Z stacks.

ImageC is able to process up to 10 channels C with any number of images in the Z stack using the Max. intensity projection algorithm. Time stacks are not yet supported. If an image with time stack is processed ony the first image of the T stack is used.

A channel is invariably associated with a channel in an image in the range of 0 to 9. The OME metadata of an image provides information regarding the number of channels present within the image and the number of Z and potentially T stacks assigned to each channel.

In order to facilitate the configuration of the channel, the OME meta date, inclusive of the channel data, is displayed on the right-hand side of the overview panel.

Slots

A slot is defined as a kind of virtual channel. It is not a physical entity within an image; rather, it is generated based on the information contained in the image channels. Slots are identified by an index in the range of A to F.

In the actual release 1.0.0-alpha.105 of ImageC two types of slots are available: Voronoi and Intersection.

Note

The input of a slot channel is the output of an image channel!

Caution

It is imperative that each channel and slot index is unique, as is each channel and slot name. Otherwise an error occurs when trying to start the analysis.