Slice-o-matic Software
Slice-o-matic Software - Related Videos
13:35
Segmentation and Linear Measurement for Body Composition Analysis using Slice-O-Matic and Horos
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Cited by 22 •
2021
Segmentation and linear measurements quantify skeletal muscle mass and adipose tissues using Computed Tomography and/or Magnetic Resonance Imaging images. Here, we outline the use of Slice-O-Matic software and Horos image viewer for rapid and accurate analysis of body composition. These methods can provide important information for prognosis and risk stratification.
10:06
Slice Preparation, Organotypic Tissue Culturing and Luciferase Recording of Clock Gene Activity in the Suprachiasmatic Nucleus
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Cited by 32 •
2011
The procedure of preparing slices containing the adult mouse hypothalamic suprachiasmatic nucleus (SCN), and a rapid way to culture the SCN tissue in organotypic culture condition, are reported. Further, the measurement of oscillatory clock gene protein expression using dynamic luciferase reporter technology is described.
10:41
VisualEyes: A Modular Software System for Oculomotor Experimentation
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Cited by 28 •
2011
Neural control and cognitive processes can be studied through eye movements. The VisualEyes software allows an operator to program stimuli on two computer screens independently using a simple, custom scripting language. The system can stimulate tandem eye movements (saccades and smooth pursuit) or opposing eye movements (vergence) or any combination.
07:59
The Analysis of Purkinje Cell Dendritic Morphology in Organotypic Slice Cultures
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Cited by 15 •
2012
We present a protocol that permits to view and to quantitatively asses the morphology of the dendritic tree of individual Purkinje cells grown in organotypic cerebellar slice cultures. This protocol is intended to promote studies on the mechanisms of Purkinje cell dendritic development.
05:02
Cerebellum Dissection and Slice Preparation: A Method to Generate Tissue Slices from Mouse Cerebellum
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2025
This video describes a method to generate tissue slices from the mouse cerebellum. The cerebellar slices can be used for organotypic culturing that provides insights into neurodevelopmental mechanisms, including myelination dynamics.
FAQs
Manual tools let users delineate a region of interest directly on individual image slices, while assisted tools support the same labeling task. The resulting measurements depend on how consistently anatomical boundaries are identified across the dataset. Keeping the labeling approach consistent helps produce more reproducible estimates of tissue, tumor, or body-composition volumes.
Slice-o-matic Software links labeled regions across serial CT or MRI slices and reconstructs them as three-dimensional models. This connection allows a structure identified on separate cross-sectional images to be evaluated as a combined volume rather than as isolated areas. Researchers can then quantify the reconstructed region and use its measurements in imaging studies.
Slice-by-slice annotation preserves the location and extent of a structure throughout a cross-sectional dataset. Users can inspect how a region appears on successive images and mark its boundaries before reconstruction. This is important when the goal is to compare anatomical structures, quantify tissue volumes, or generate labeled data for biomedical analysis.
A typical workflow begins by displaying the serial CT or MRI slices, followed by identifying and delineating the region of interest with manual or assisted tools. The labeled regions are then reconstructed into three-dimensional models for measurement. Users may also annotate or compare regions, creating quantitative outputs suitable for clinical or biomedical research.
The platform can support studies that require measurements of tissue volumes, body composition, tumors, and other anatomical structures. Its labeling and reconstruction workflow turns image data into quantitative results that can be examined across subjects, regions, or datasets. This makes it relevant to research focused on anatomical assessment and imaging-based biomedical analysis.
Beyond measuring structures, Slice-o-matic Software supports annotation and preparation of labeled imaging datasets. Researchers can mark relevant regions, organize their spatial information across image slices, and reconstruct those labels for analysis. These outputs can help create more structured datasets for clinical investigations, biomedical research, and comparisons of anatomical findings.