Display Platemap displays a desired measurement in a plate map view.
Display Platemap is a tool for browsing image-based data laid out on multi-well plates common to high-throughput biological screens. The display window for this module shows a plate map with each well color-coded according to the measurement chosen.
As the pipeline runs, the measurement information displayed is updated, so the value shown for each well is current up to the image cycle currently being processed; wells which have no corresponding measurements as yet as shown as blank.
See also DisplayDensityPlot, DisplayHistogram, DisplayScatterPlot.
Settings:
Display object or image measurements?
- Image allows you to select an image
measurement to display for each well.
- Object allows you to select an object measurement to display
for each well.
Select the object whose measurements will be displayed
Choose the name of objects identified by some previous
module (such as IdentifyPrimaryObjects or
IdentifySecondaryObjects) whose measurements are to be displayed.
Select the measurement to plot
Choose the image or object measurement made by a previous module to plot.
Select your plate metadata
Choose the metadata tag that corresponds to the plate identifier. That is,
each plate should have a metadata tag containing a specifier corresponding
uniquely to that plate.
Please see the Metadata module for more details on metadata collection and usage.
Multiwell plate format
The module assumes that your data is laid out in a multi-well plate format
common to high-throughput biological screens. Supported formats are:
- 96: A 96-well plate with 8 rows × 12 columns
- 384: A 384-well plate with 16 rows × 24 columns
Select your well metadata
Choose the metadata tag that corresponds to the well identifier.
The row-column format of these entries should be an
alphabetical character (specifying the plate row), followed by two integer
characters (specifying the plate column). For example, a standard format
96-well plate would span from "A1" to "H12", whereas a 384-well plate (16
rows and 24 columns) would span from well "A01" to well "P24"."
Please see the Metadata module for more details on metadata collection and usage.
Select your well row metadata
Choose the metadata tag that corresponds to the well row identifier, typically
specified as an alphabetical character. For example, a standard format
96-well plate would span from row "A" to "H", whereas a 384-well plate (16
rows and 24 columns) would span from row "A" to "P".
Please see the Metadata module for more details on metadata collection and usage.
Select your well column metadata
Choose the metadata tag that corresponds to the well column identifier, typically
specified with two integer characters. For example, a standard format
96-well plate would span from column "01" to "12", whereas a 384-well plate (16
rows and 24 columns) would span from column "01" to "24".
Please see the Metadata module for more details on metadata collection and usage.
How should the values be aggregated?
Measurements must be aggregated to a
single number for each well so that they can be represented by a color.
Options are:
- avg: Average
- stdev: Standard deviation
- median
- cv%: Coefficient of variation, defined as the ratio of the standard
deviation to the mean. This is useful for comparing between data sets with
different units or widely different means.
Enter a title for the plot, if desired
Enter a title for the plot. If you leave this blank,
the title will default
to (cycle N) where N is the current image
cycle being executed.
Well metadata format
- Well name allows you to select an image
measurement to display for each well.
- Row & Column allows you to select an object measurement to display
for each well.