par-segmentation 0.1.4

Cell cortex segmentation in C. elegans PAR protein images

PAR Segmentation

Tools for segmenting and straightening the cortex of cells from midplane images using a gradient descent algorithm. Designed primarily for use on images of PAR proteins in C. elegans zygotes.

Methods

Starting with an initial rough manual ROI of the cell edge, the cortex of the image is straightened (Step 1). The program then attempts to mimic this straightened image by differentiable simulation (Step 2). In doing so, it learns the position of the cortex, which enables the ROI to be adjusted (Step 3) and the cortex re-straightened.

Cortex positions are modelled as a spline with a user specified number of knots which are optimised by gradient descent:

The program additionally outputs parameters related to cytoplasmic and membrane concentrations, so can serve as a quantification tool as well as a segmentation tool:

The differentiable simulation is built on the assumption that cross-cortex intensity profiles at each position around the cortex are the sum of distinct cytoplasmic and membrane signal components. Here, we model these two components as an error function and Gaussian function respectively, representing the expected shape of a step and a point convolved by a Gaussian point spread function (PSF) in one dimension. This is a slight simplification of reality, and doesn't account for the possibility of a non-Gaussian PSF and complex light-scattering behaviours, but is a close enough approximation for many purposes.

Nevertheless, we can relax these assumptions if higher quantification accuracy is required. See here for an extension of the method designed for more accurate quantification.

Installation

pip install par-segmentation

Instructions

See the tutorial notebook here

To run in the cloud click 'launch binder' at the top

Publications

Code in this repository has been used in the following publications for PAR protein segmentation and/or quantification:

Illukkumbura, R., Hirani, N., Borrego-Pinto, J., Bland, T., Ng, K., Hubatsch, L., McQuade, J., Endres, R.G., and Goehring, N.W. (2022). Design principles for selective polarization of PAR proteins by cortical flows. BioRxiv 2022.09.05.506621.

Ng, K., Hirani, N., Bland, T., Borrego-pinto, J., and Goehring, N.W. (2022a). Cleavage furrow-directed cortical flows bias mechanochemical pathways for PAR polarization in the C . elegans germ lineage. BioRxiv 1–32.

Ng, K., Bland, T., Hirani, N., and Goehring, N.W. (2022b). An analog sensitive allele permits rapid and reversible chemical inhibition of PKC-3 activity in C . elegans. MicroPublication Biol.

Rodrigues, N.T.L., Bland, T., Borrego-Pinto, J., Ng, K., Hirani, N., Gu, Y., Foo, S., and Goehring, N.W. (2022). SAIBR : A simple, platform-independent method for spectral autofluorescence correction. Development.

License

This work is licensed under a Creative Commons Attribution 4.0 International License.