![tophat method cellprofiler tophat method cellprofiler](https://tophat.com/wp-content/uploads/Webinar_Remote-Testing_20202.jpg)
A processing chain is composed of three steps: pre-processing, segmentation and post-processing, as detailed in Supplementary Figure S2. detection of nuclei and nuclear structures, is achieved by applying a processing chain to the associated image. For performance and usability, all images and parameters are stored in a MongoDB database, a highly powerful document-oriented system ( ). This pre-defined workflow simplifies the workload: TANGO only requires specification of the number of channels, then the definition of associated structures. This results in an hierarchical organization of data: fields contain nuclei, which contain structures, which can contain segmented objects. S1): segmentation of nuclei, followed by segmentation of structures within each nucleus (when needed). The processing workflow is composed of two successive steps ( Supplementary Fig. All image files compatible with Bio-formats ( ) (>100 formats) can be imported to TANGO. Each channel corresponds to a fluorescent marker and can be associated with a biological compartment of interest (further termed structure).
![tophat method cellprofiler tophat method cellprofiler](https://i1.rgstatic.net/publication/345821040_Rolling_Bearing_Fault_Diagnosis_Method_With_Enhanced_Top-Hat_Transform_Filtering_and_Cyclic_Spectrum_Coherence/links/604eba9a458515e529abda09/largepreview.png)
The input data of TANGO consists of multichannel Z-stack images of microscopy fields, containing one or several nuclei. 2 IMAGE PROCESSING 2.1 Data organization and general workflow
![tophat method cellprofiler tophat method cellprofiler](https://thm-monocle-interactive.s3.amazonaws.com/RW6hedVZv7%2FPicture1.png)
A potential application is the study of radial position variations of various structures (such as genes or centromeres) with respect to the nuclear membrane or to nucleoli, throughout the cell cycle. To overcome these limitations, we have developed Tools for Analysis of Nuclear Genome Organization (TANGO), an image analysis framework, which permits biologists to perform the complete analysis process of 3D fluorescence images: image processing, quantitative analysis and statistical processing. FishFinder ( Shirley et al., 2011) and NEMO ( Iannuccelli et al., 2010) perform 3D analysis but have limited image processing and analysis capabilities. CellProfiler ( Kamentsky et al., 2011), which is one of the most popular, only performs 2D analysis.
#TOPHAT METHOD CELLPROFILER SOFTWARE#
Several software programs have already been developed. Though recent microscopes facilitate the acquisition of large sets of 3D images, the automatic processing and analysis of those images remains a difficult task. For example, immunocytochemistry and fluorescence in situ hybridization (FISH) allow the selective fluorescent labeling of protein-enriched compartments and chromosomal domains, respectively. Nuclear organization can be studied using several imaging techniques. The underlying mechanisms are still a matter of extensive investigation. The spatial localization of genes and nuclear compartments within the nucleus affects cellular functions, such as regulation of gene expression, DNA replication and repair ( Austin et al., 2010). The nucleus is a heterogeneous and compartmentalized organelle. Distribution is under the GPL v.2 licence.Ĭontact: information: Supplementary data are available at Bioinformatics online.
#TOPHAT METHOD CELLPROFILER FREE#
They are both free and open source, available ( ) for Linux, Microsoft Windows and Macintosh OSX. TANGO is a versatile tool able to process large sets of images, allowing quantitative study of nuclear organization.Īvailability: TANGO is composed of two programs: (i) an ImageJ plug-in and (ii) a package (rtango) for R. It includes an intuitive user interface providing the means to precisely build a segmentation procedure and set-up analyses, without possessing programming skills. TANGO is a coherent framework allowing biologists to perform the complete analysis process of 3D fluorescence images by combining two environments: ImageJ ( ) for image processing and quantitative analysis and R ( ) for statistical processing of measurement results. Results: Here, we describe Tools for Analysis of Nuclear Genome Organization (TANGO), an image analysis tool dedicated to the study of nuclear architecture. However, such approaches are limited by the requirement for processing and analyzing large sets of images. Extracting quantitative data from 3D fluorescence imaging helps understand the functions of different nuclear compartments. The study of nuclear architecture has become an important field of cellular biology. Motivation: The cell nucleus is a highly organized cellular organelle that contains the genetic material.