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MotionTracking Reader

HCS-Tools for KNIME version 4.0.0.v202007151505 by Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

Reads a list of MotionTracking '.csv'-export-files into Knime. This is done by searching for csv-files recursively within the specified directory or by selecting a list of files directly.

Options

Input Files

There are two modes of operation. Either you can choose a single directory in which the nodes will search for MotionTracking files. The search is applied not only to the direct directory contents but also to also its subfolders.
The second mode is to select a set of files (by keeping the apple/windows-key pressed while selecting files).
In the advanced tab of the configuration dialog one can define the pattern and associate the keywords to interpret the information of the file Paths contained in the first column. The default pattern is:
(?<barcode>.*)__(?<row>[0-9]{3})(?<column>[0-9]{3})[0-9]{3}_(?<timpoint>[0-9]{1})(?<wellfield>[0-9]{3})[.]mtf
This pattern matches file paths from images acquired with the Opera (Perkin Elmer) and that are converted with motion tracking into mtf-files. Anything that is contained within () -> token, will be associated with the variable that is contained within. The rest of the syntax is normal regular expressions (see java-doc).

The mandatory variables are
barcode
row
column

The optional variables are:
timepoint: time point between scans
wellfield: field of view within one well
frame: can be a time-frame of a movie or a z-slice of a z-stack (usually not used in HCS).

Thus another example for the same type of paths:
(?<barcode>.*)__(?<row>[0-9]{3})(?<column>[0-9]{3})(?<frame>[0-9]{3})_(?<timpoint>[0-9]{1})(?<wellfield>[0-9]{3})[.]mtf

Output Ports

Icon
The imported MotionTracking-data

Best Friends (Outgoing)

Installation

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

KNIME 4.3

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

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Developers

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