Farsight Courses OneWeek
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= Learning Objectives = | = Learning Objectives = | ||
| − | * | + | * Upon successful completion of this course, the participants will have a working knowledge of how to apply freely available open-source computational image analysis tools (FARSIGHT, ITK, VTK, Paraview, Overview) to generate quantitative measurements from 3D/4D/5D microscopy image data. |
| + | * Specifically, | ||
| + | ** Ability to read, visualize and write images files for various common formats. | ||
| + | ** Ability to design computational scripts for image pre-processing to correct for common imaging artifacts (noise, blur, spectral overlap). | ||
| + | ** Being able to segment common types of biological objects (cell, nuclei, membranes, micro-vasculature, neurites, foci) in 2D and 3D images of cells and tissue. | ||
| + | ** Being able to perform edit-based validation of segmentation results. | ||
| + | ** Being able to perform registration and montaging. | ||
| + | ** Being able to perform cell and organelle tracking, and analysis of changes in time-lapse image series. | ||
| + | ** Being able to compute morphological measurements of biological objects. | ||
| + | ** Being able to compute associative measurements linking two or more biological objects. | ||
| + | ** Being able to summarize and conduct statistical analysis of measurements. | ||
= Pre-requisites = | = Pre-requisites = | ||
Revision as of 14:04, 18 September 2009
Contents |
Audience
- Researchers in academic & industrial laboratories who make active use of optical microscopes, and desire to make image-based quantitative measurements for hypothesis testing, screening, and modeling
- Particular emphasis is placed on fluorescence based multi-dimensional microscopy (3-D confocal/multi-photon, time-lapse, multi-channel, etc.)
- This course will provide instruction on biological image analysis concepts/theory, and hands-on practical learning.
Learning Objectives
- Upon successful completion of this course, the participants will have a working knowledge of how to apply freely available open-source computational image analysis tools (FARSIGHT, ITK, VTK, Paraview, Overview) to generate quantitative measurements from 3D/4D/5D microscopy image data.
- Specifically,
- Ability to read, visualize and write images files for various common formats.
- Ability to design computational scripts for image pre-processing to correct for common imaging artifacts (noise, blur, spectral overlap).
- Being able to segment common types of biological objects (cell, nuclei, membranes, micro-vasculature, neurites, foci) in 2D and 3D images of cells and tissue.
- Being able to perform edit-based validation of segmentation results.
- Being able to perform registration and montaging.
- Being able to perform cell and organelle tracking, and analysis of changes in time-lapse image series.
- Being able to compute morphological measurements of biological objects.
- Being able to compute associative measurements linking two or more biological objects.
- Being able to summarize and conduct statistical analysis of measurements.
Pre-requisites
- Familiarity with contemporary computers PC/Mac/Linux
- Basic knowledge of programming using scripting languages
- We will use Python
- Familiarity with common viewing tools and file formats
