Microscopy

Cohesin depleted cells pass through mitosis and reconstitute a functional nuclear architecture.

The human genome forms thousands of “contact domains”, which are intervals of enhanced contact frequency. Some, called “loop domains” are thought to form by cohesin-mediated loop extrusion. Others, called “compartmental domains”, form due to the …

Co-localization analysis in fluorescence microscopy via maximum entropy copula

Co-localization analysis is a popular method for quantitative analysis in fluorescence microscopy imaging. The localization of marked proteins in the cell nucleus allows a deep insight into biological processes in the nucleus. Several metrics have …

bioimagetools

R tools for working with images in 3D and 4D, mostly for biology/microscopy.

nucim

Nucleome Imaging Toolbox is an R package for quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

Background: The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an open local chromatin configuration has long been known. However, the 3D topography of TREs within the nuclear landscape of …

Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy

Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools …

Stage-dependent remodeling of the nuclear envelope and lamina during rabbit early embryonic development

Utilizing 3D structured illumination microscopy, we investigated the quality and quantity of nuclear invaginations and the distribution of nuclear pores during rabbit early embryonic development and identified the exact time point of nucleoporin 153 …

Bayesian mixed-effects model for the analysis of a series of FRAP images

The binding behavior of molecules in nuclei of living cells can be studied through the analysis of images from fluorescence recovery after photobleaching experiments. However, there is still a lack of methodology for the statistical evaluation of …

Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications

The present study demonstrates a major remodeling of the nuclear envelope and its underlying lamina during bovine preimplantation development. Up to the onset of major embryonic genome activation (MGA) at the 8-cell stage nuclei showed a non-uniform …

Reprogramming of fibroblast nuclei in cloned bovine embryos involves major structural remodeling with both striking similarities and differences to nuclear phenotypes of in vitro fertilized embryos