Plate Heatmap Viewer

Creates trellis of heatMaps to explore your screen. By default nodes expects three columns to be present in order to reorder wells back into plates:
- barcode
- plateRow
- plateColumn

Supported microtiter plate formats:
6, 12, 24, 96, 384 and 1536. The viewer will try to make a guess about the proper plate dimension if not all wells are present in the table (e.g. because outer rows are not used).

Image data:
Tables containing images allow visualization of the well images in the well detail view. Any cell of an image data column will be visualized. So far the KNIME native PNG images are recognised, as well as the formats provided by the Image Processing plugin. Careful! the processing might take time and disk space. The best performance is achieved with the "Image Reference" produced by the "Image File Linker" node of the image processing plugin.

Options

Readouts

A selection of readouts which should be displayed by the viewer. Especially for high-content screens with many readouts (100+), you may want to include just a subset them. This will help to prevent memory problems.

Factors

Annotation column that further characterize the wells.

Barcode

Select column to assign barcode (string or integer).

Row

Select column to assign row value (integer, 1 to 16 refers to A to P).

Column

Select column to assign column value (integer, 1 to 24).

Plate Label

Column that is used to extract the plate label, which should allow easy identification of the plate.

Controls

The subset column allows to choose a nominal attribute, which allows to identify control populations.
Select one ore several reference groups. These can be used to define custom color maps (gray out or mark the populations range with a special color).

Input Ports

A table containing High Content Screening data.

Output Ports

Same as input table.

PNG image of the heatmap trellis containing all plates. It takes the first readout in the list, the default colormap and no overlay.

Views

Plate Heatmap Trellis

Trellis containing all heatmaps representing the plates of the screen.

Mouse behaviour:
The heatmap trellis and the individual plate view support single selection and drag-selection.
Right click on a plate of the trellis opens an individual plate view. A right click on a well of the plate view opens an a well detail view.

Best Friends (Incoming)

• GroupBy (7 %) 
• Row Filter (6 %) Streamable
• Expand Well Position (5 %) Deprecated
• Concatenate (4 %) Streamable
• Normalize Plates (POC) (4 %) 
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Best Friends (Outgoing)

• HiLite Row Splitter (14 %) 
• HeatMap (JFreeChart) (6 %) 
• Row Splitter (5 %) Streamable
• Table Writer (5 %) 
• Image Writer (Port) (5 %) 
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Workflows

• 01_​Visualization_​of_​screening_​data (KNIME Hub) 
• 06_​Visualization_​of_​screening_​data_​2 (KNIME Hub) 
• HTS_​workflow (KNIME Hub) 
• NucleiClassificationTraining (KNIME Hub) 
• NucleiClassificationTraining_​OMICS2020 (KNIME Hub) 

Installation

To use this node in KNIME, install KNIME HCS Tools from the following update site:

A zipped version of the software site can be downloaded here.

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Developers

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