Key concepts: Cells are grown in a 384-well plate and therefore a Plate is an important unit of data as all samples from a single plate will share some level of technical artifacts. Each Well within the plate contains a single perturbation (e.g. each well is given a different drug). Within each Well there are multiple fields of view acquired by the microscope which we generally call Sites. Each Site will have images acquired in a set of Channels - a channel is a specific light path within a microscope and, when combined with specific fluorescent labels on a sample, represents specific biology that we are observing.
Module overview: This module is typically run in Fiji but it is not a requirement that this implementation use Fiji if a similar output can be produced by different software. This step takes the images produced by the cellprofiler_assaydev step and stitches them into a a pseudo-Plate view that makes it easy for a biologist to visually inspect all of the outputs at a glance.
This module takes as inputs:
- images (the outputs of the cellprofiler_assaydev step)
It produces the output of the input images stitched into a pseudo-Plate view.
Key concepts: Cells are grown in a 384-well plate and therefore a
Plateis an important unit of data as all samples from a single plate will share some level of technical artifacts. EachWellwithin the plate contains a single perturbation (e.g. each well is given a different drug). Within eachWellthere are multiple fields of view acquired by the microscope which we generally callSites. EachSitewill have images acquired in a set ofChannels - a channel is a specific light path within a microscope and, when combined with specific fluorescent labels on a sample, represents specific biology that we are observing.Module overview: This module is typically run in Fiji but it is not a requirement that this implementation use Fiji if a similar output can be produced by different software. This step takes the images produced by the cellprofiler_assaydev step and stitches them into a a pseudo-
Plateview that makes it easy for a biologist to visually inspect all of the outputs at a glance.This module takes as inputs:
It produces the output of the input images stitched into a pseudo-
Plateview.