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Outer cell layer of fly embryo is analyzed in 3D. individual cells are segmented and highlighted in different colors. Cell volume is visualized on the top left half while cell motion tracks are seen at the bottom right half.
IMAGE ANALYSIS EXAMPLES

Image Analysis Examples for Developmental Biology

Developmental biology delves into the complex processes that govern the growth and differentiation of organisms. At its core, this field relies heavily on advanced imaging technologies and powerful image analysis software to observe and document the minutest details of developmental stages.

By using diverse algorithms, filters and measurements you can easily define and quantify various relationships. Then easily visualize and display them in graphs and diagrams. Create flexible, end-to-end pipelies to answer research questions with just a few clicks.

Easy-to-use tools and functions help you streamline your image analysis for developmental biology applications. From routine tasks to in-depth exploration, our powerful software helps you accelerate your time to market.

Tracks of cells in a developing fly embryo color-coded by average track speed, in diverse colors ranging from green and yellow to cyan and blue with highlights of red.

Dynamics and Tracking

Track objects of diverse size and measure varied parameters for fast, reproducible results with full control and interactivity

Automation is the key for tracking complex biological data. The Tracking Module in ZEISS arivis Pro allows analysis of the movement of small (i.e. particle tracking) or large objects (e.g. nuclei, cells, organisms) over time in both 2D or 3D multichannel image sets of any size (100s of GBs or TBs). You can track various parameters and apply diverse measurements. For example: velocity and average speed, motion types, automatic detection of maximum distance, vector display (head and tail), adjustable weighting, divisions over time and more.

Automated tracking algorithms deliver high performance. Combined with AI-driven segmentation, and enhanced proofreading features to enable tracking and lineage analysis of multidimensional data sets. You can quickly gain reproducible results and meaningful output for any kind of tracking task.

Cells membranes segmented highlighted in green.

These data were kindly provided by Tsung-Li Liu, Srigokul Upadlyayula, Tom Kirchhausen, and Eric Betzig and appear in their excellent paper: “Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms”

Membrane-based Segmentation

Finding Cell Boundaries Based on Membrane-Localized Contrast in 3D

Finding cell boundaries based on membrane-localized contrast is made many times easier by new algorithms that enhance membranes in 3D and an operator designed to segment cells in 3D. This new workflow allows use of any image filters upstream of the Membrane-based Segmentation, which enables optimization of results and/or application to challenging images.

Users can select between Membrane Enhancement and Objectness Measure (sheets) filters, depending on data quality and time constraints. The Membrane Enhancement filter gives the highest quality but takes longer while The Objectness Measure feature computes faster. The Membrane-based Segmentation is adjusted interactively to increase cell segmentation yield and “over splitting” is easily proof-edited with the Merge tool. All the other filters in (formerly Vision4D) - Morphology, Denoising, etc. - are at the users’ disposal for fine tuning.

Chart in Object Table is an extremely powerful analysis tool which allows users to quickly gain insight about object interaction in their data.

Subcellular Object Interaction Analysis

The New Chart in Object Table Allows Users to Visualize One or Two Features from Either All or Selected Objects in the Table and a Graph

The Chart in Object Table allows users to graph one or two features from either all or selected objects in the table. Using the Object Selection and the Color tool from Object Table enhances the sophisticated usage with the Chart Visualization tool. In this example, a particular subject of objects in our image is highlighted with color coding.

This helps users to understand the object-object interactions and helps users to tell a more complete story about their image. Here are some examples and ideas of how you can use tools in ZEISS arivis Pro Object Table to tell others about your remarkable data. Only ZEISS arivis Pro can offer the power to fully understand the dynamic relationships in your data using the power of chart selection and on-screen interactive 3D visualization.

Further Applications

Nuclei and micronuclei segmented in an embryo, on the left you see the green, fluorescent raw image and on the right the 3D analysis of sub cellular structures.
18 September 2022

Cell Phenotype Image Analysis for Cancer Research and Cell Biology

Applications Hub - 6 min read
ZEISS Microscopy
3D preview of analysis results in which individual cells in the outer layer of an organoid are visualized in different colors.
16 September 2024

Image Analysis Examples for Organoid Growth Analysis

Applications Hub - 10 min read
ZEISS Microscopy
A neuron cell in the brain is traced and marked in a microscopy image in 3D view. The cell body is in the center and neurite branches sprout of it.
16 September 2024

Automate your Neuron Tracing Image Analysis Workflows

Applications Hub - 3 min read
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    * The images shown on this page represent research content. ZEISS explicitly excludes  the possibility of making a diagnosis or recommending treatment for possibly affected  patients  on the basis of  the information generated with an Axioscan 7 slide scanner.