Compute nuclear chromatin distribution in zygotes
Abstract
The workflow computes metrics of the chromatin distribution in the two nuclei of a zygote before nuclear envelope breakdown. The metrics are - Inner/outer fractions: Quantify chromatin intensities in oriented sections of the nucleus. The sections are oriented in the direction of the 2 nuclei. - Maximal polarity: Find an orientation along each nuclei that maximizes the chromatin fraction in one of the sections. - Nuclear occupancy: Quantifies the amount of chromatin with respect to the total volume of the nucleus. - Surface occupancy: Quantifies chromatin intensity in a region close to the surface with respect to inside of the nucleus. The workflow uses different software and plugins. In short, starting from a .czi file the user has to 1. Prepare data for processing (IJ script SplitTpointsH2bchannel.ijm) 2. Manually specify nuclei masks using spheres (IJ script BoneJFitSphere.ijm) 3. Compute the maximal polarity (IJ plugin nuclei polarity) 4. Segment and compute the distribution of the chromatin mass (Matlab code computePoiDistribution.m)_
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