Hemichannel dye uptake assay image analysis software
- 1. ETH Zurich, Paul Scherrer Institute
Description
The script was generated for processing of connexin HC dye uptake fluorescent microscopy data, in which each field of view contains three images collected by three different dye channels: a nuclear channel, a YFP channel (indicator channel) and a connexin-permeable dye channel.
- The nuclei serve as regions of interest (ROIs),
- YFP channel as an indicator of the target cells, which contain the connexin (indicator channel),
- SR101 (connexin-permeable dye) channel as an indicator of connexin function and the channel, from which the measurement is taken from (measurement channel).
The script is useful for all other purposes, in which the measurement is taken in the nucleus region of the cell from a non-nucleus channel (measurement channel), in which only a subset of nuclei are of interest, based on an indicator channel.
The script contains the following processing steps:
a. Pre-processing (scaling of all images to the size of the model (360x360 pix) and normalisation of the nucleus channel);
b. Segmentation of the nuclei and generation of a mask covering the nuclei ROIs;
c. Elimination of nuclei ROIs, which are not of interest (signal in indicator channel is below threshold);
b. Measurement of signal from measurement channel, from final ROIs.
This work is based on the StarDist 2D nuclear segmentation method for nuclear segmentation.
Files
experimenal-pipeline.png
Files
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Additional details
Related works
- Is derived from
- Journal article: 10.1007/978-3-030-00934-2_30 (DOI)
- Is part of
- Journal article: 10.1126/sciadv.adh4890 (DOI)
References
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- Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357–362 (2020). DOI: 10.1038/s41586-020-2649-2.
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