About
OpenSegSPIM is an open access and user friendly 3-D automatic quantitative analysis tool for nuclei and cell membranes. It is designed to be as accessible as possible.
OpenSegSPIM
The software is designed to extract quantitative relevant information from SPIM image stacks, such as the number of nuclei/cells and provide quantitative measurement (Volume, sphericity, distance, intensity) on Light Sheet Microscopy (LSM) images. Typically, it is a useful quantitative analysis tool for different biological samples such as Neurospheres, Zebrafish embryos, Drosophila embryos, Skin sample, Mouse embryos and other organotypic cell culture.
The OpenSegSPIM pipeline (see Figure 1) consists of a succession of step each one being enabled once the previous step has been completed. To provide a simple interface OpenSegSPIM minimizes the number of parameters without loss of segmentation quality. Furthermore, parameter input is an interactive process. For example, image smoothing is done in a few steps and the user only needs to measure the diameter of the nuclei. To facilitate the difficult step of parameter tuning the intermediate results are visualized in real time and can be evaluated.
The OpenSegSPIM pipeline (see Figure 1) consists of a succession of step each one being enabled once the previous step has been completed. To provide a simple interface OpenSegSPIM minimizes the number of parameters without loss of segmentation quality. Furthermore, parameter input is an interactive process. For example, image smoothing is done in a few steps and the user only needs to measure the diameter of the nuclei. To facilitate the difficult step of parameter tuning the intermediate results are visualized in real time and can be evaluated.