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

Icon
A table containing High Content Screening data.

Output Ports

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

Popular Predecessors

  • Expand Well Position9 %
  • String To Number4 %
  • CSV Reader4 %
  • File Reader3 %
  • Number To String2 %
  • Linear Correlation2 %
  • Join Layout2 %
  • k-Means2 %
  • Missing Value2 %
  • Example Data2 %
  • Heatmap2 %
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  • Column Rename (Regex)2 %
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  • Normalize Plates (NPI)1 %
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  • BinningAnalysis< 1 %
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  • Concatenate (Optional in)< 1 %
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  • Fingerprint Similarity< 1 %
  • Read Images< 1 %
  • Table Row To Variable Loop Start< 1 %
  • Expand Byte Vector< 1 %
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  • Regex Split< 1 %
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Popular Successors

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.

Workflows

Links

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

Installation

To use this node in KNIME, install the extension KNIME HCS Tools from the below update site following our NodePit Product and Node Installation Guide:

v5.12
Plugin provider: Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
Plugin version: 5.5.0.v202511111303
On NodePit since: 2026-07-06
Last update: 2026-08-01
KNIME versions: v5.12, v5.11, v5.10, v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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