History Analysis of solitary cells in their native environment is a powerful method to address important questions in developmental systems biology. cell fate specification and morphogenesis: the pre-implantation mouse embryo and the developing mouse olfactory epithelium. We statement a pipeline that integrates machine-learning-based cell detection fast human-in-the-loop curation of these detections and operating of active contours seeded from detections to section cells. The procedure can be bootstrapped by a small number of manual detections and outperforms alternate pieces of software we benchmarked on gonad datasets. Using cell segmentations to quantify fluorescence material we statement NVP-BGT226 previously-uncharacterized cell behaviors in the model systems we used. We further show how cell morphological features can be used to determine cell cycle phase; this provides a basis for future tools that may streamline cell cycle experiments by minimizing the need for exogenous cell cycle phase labels. Conclusions High-throughput 3D segmentation makes it possible to extract rich info from images that are regularly acquired by biologists and provides insights – in particular with respect to the cell cycle – that would be hard to derive normally. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0814-7) contains supplementary material which is available to authorized users. germ collection Mouse pre-implantation embryo Olfactory placode Olfactory epithelium Background Understanding the mechanisms by which cells make proliferation and differentiation decisions is definitely a query of important interest to systems developmental and stem cell biologists. Individual cells display rich cycling and differentiation behaviors that RHEB are often not deterministic – as illustrated by stochastic transitions between different progenitor claims [1-3] – and that are obscured in human population averages. Furthermore cell proliferation and differentiation are controlled to a large degree by extracellular cues that often can be only very partially and crudely reproduced in vitro. To better understand the mechanisms root cell proliferation and differentiation brand-new tools are hence necessary to quantify the behavior of one cells within their indigenous tissue environments. Many techniques currently utilized to quantify properties of specific cells – such as for example stream cytometry NVP-BGT226 – depend on tissue being dissociated ahead of evaluation which destroys the spatial and morphological details within the sample. These resources of information are conserved by imaging of undissociated organs or tissue; such imaging can be carried out easily with current NVP-BGT226 technology (e.g. confocal microscopy) nonetheless it does not instantly result in cell-by-cell details without comprehensive analysis to portion specific cells in the causing three-dimensional (3D) pictures. Here we survey the overall technique that we have got followed to review the spatial distribution of cell routine or cell differentiation properties in three different tissue: the germ series the mouse pre-implantation embryo as well as the mouse olfactory epithelium. While there is an ever growing set of biological image segmentation software solutions that tackle this problem we found that the guidelines of NVP-BGT226 these systems were often hard to tune and that most did not offer the capability to by hand curate intermediate results during processing. NVP-BGT226 To accomplish accurate in vivo cytometry we therefore chose to develop our own software built on verified powerful algorithms for image analysis to keep up maximal flexibility in the integration of automated processing and manual labeling effort. A number of general image segmentation tools exist that are specifically targeted at biological applications including both open resource [4-18] and commercial software (e.g. Imaris Bitplane or Volocity PerkinElmer). For more considerable surveys observe e.g. [18-20]. Despite quick development (observe e.g. cell tracking benchmark competition ) the problem of instantly generating high-quality 3D segmentations of cells in general images remains unsolved due to the wide variance in appearance across different cells and cell types labeling methods and imaging methods. Rather than tuning existing NVP-BGT226 pipelines or developing custom segmentation algorithms that might improve overall performance on images of particular cell types we decided to design a pipeline that maximizes the energy of the.