e-learning
Nucleoli segmentation and feature extraction using CellProfiler
Abstract
The nucleolus is a prominent structure of the nucleus of eukaryotic cells and is involved in ribosome biogenesis and cell cycle regulation. In DNA staining of cells, nucleoli can be identified as the absence of DNA in nuclei (Fig. 1).
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How do I run an image analysis pipeline on public data using CellProfiler?
- How do I analyse the DNA channel of fluorescence siRNA screens?
- How do I download public image data into my history?
- How do I segment and label cell nuclei?
- How do I segment nucleoli (as the absence of DNA)?
- How do I combine nuclei and nucleoli into one segmentation mask?
- How do I extract the background of an image?
- How do I relate the nucleoli to their parent nucleus?
- How do I measure the image and object features?
- How do I measure the image quality?
Learning Objectives
- How to download images from a public image repository.
- How to segment cell nuclei using CellProfiler in Galaxy.
- How to segment cell nucleoli using CellProfiler in Galaxy.
- How to extract features for images, nuclei and nucleoli.
Licence: Creative Commons Attribution 4.0 International
Keywords: Imaging
Target audience: Students
Resource type: e-learning
Version: 9
Status: Active
Prerequisites:
- FAIR Bioimage Metadata
- Introduction to Galaxy Analyses
- REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
Learning objectives:
- How to download images from a public image repository.
- How to segment cell nuclei using CellProfiler in Galaxy.
- How to segment cell nucleoli using CellProfiler in Galaxy.
- How to extract features for images, nuclei and nucleoli.
Date modified: 2024-10-15
Date published: 2020-07-01
Scientific topics: Imaging
External resources:
Activity log
