Farsight Courses OneWeek
From FarsightWiki
Contents |
Intended 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 microscopy and multi-dimensional microscopy (3-D confocal/multi-photon, time-lapse, multi-channel, etc.)
Instructional Methodology
This course will provide instruction on biological image analysis by combining three kinds of sessions:
- Concepts / theory presentations in lecture format
- Guided hands-on practical exercises (team oriented) as follow up to the lectures
- Participant presentations (voluntary)
- Invited speakers (to be announced)
Learning Objectives
- Upon successful completion of this course, the participants will have a working knowledge of basic open-source computational image analysis tools (FARSIGHT, ITK, VTK, Paraview, Overview) to generate quantitative measurements from 3D/4D/5D microscopy image data.
- Developing skills on the use of a selected subset of computational methods from the ITK and FARSight libraries.
- Developing awareness of more advanced tools that are part of the ITK and FARSight libraries, as well as the support resources available such as email forums and Wiki pages.
- 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
Content
Day 1
Morning
- 8:00am-9:00am Introduction and Overview (B.R.)
- 9:00am-10:00am Introduction to the Python Scripting & XML (L.I.)
- 10:00am-10:30am Break
- 10:30am-12:00pm Hands-on session 1
- Reading images from different file formats, write a few formats, & view image metadata (Use ImageJ) (C.R.)
- Image visualization methods (emphasize multi-channel, 3-D, and time-lapse datasets)
- 12:00pm-1:00pm Working Lunch
- Two participant presentations (15 min each)
Afternoon
- 1:00pm-1:20pm More Python basics (L.I.)
- 1:20pm-2:00pm Hands-on exercises on pre-processing, segmentation and visualization using Python-wrapped ITK (L.I.)
- 2:00pm-2:30pm Break
- 2:30pm-3:10pm Fundamental of image processing (B.R.)
- 3:15pm-5:00pm Hands-on session
- Pixel level image processing
- Grayscale morphology
- Image smoothing, denoising
- Deconvolution (C.P).
- Pixel level image processing
- 6:00-8:00pm Dinner
- Three participant presentations (15 min each)
Day 2
Morning
- 8:00am-9:00am Segmentation and morphometry of cell Nuclei (B.R.)
- 9:00am-10:00am Hands-on exercises with FARSight nuclear segmentation and validation tools.
- 10:00am-10:30am Break
- 10:30am-11:00am Statistical analysis of measurement data (TBD)
- 11:00am-12:00am Hands-on exercises on information visualization (Jeff?)
- 12:00pm-1:00pm Working Lunch
- Two participant presentations (15 min each)
Afternoon
- 1:00pm-2:00pm Segmentation of blood vessels (B.R./S.A.)
- 2:00pm-2:30pm Break
- 2:30pm-3:00pm Vascular morphometry (B.R./S.A.)
- 3:00pm-3:30pm More programming skills
- 3:30pm-5:00pm Hands-on exercises with FARSight and ITK tools (Team)
- 6:00-8:00pm Dinner
- Three participant presentations (15 min each)
Day 3
Morning
- 8:00am-9:00am Segmentation of neurites and astroglia (B.R.)
- 9:00am-10:00am Morphometry of neurons and astroglia (B.R./G.A.)
- 10:00am-10:30am Break
- 10:30am-12:00am Hands-on exercises with FARSight and L-Measures (Team)
- 12:00pm-1:00pm Working Lunch
- Two participant presentations (15 min each)
Afternoon
- 1:00pm-1:30pm Associative image analysis - Part I (B.R.)
- 1:30pm-2:30pm Hands-on session with FARSight and SLF tools (Sub-cellular location features)
- 2:30pm-3:00pm Break
- 3:00pm-3:30pm Pattern analysis fundamentals
- 3:30pm-4:00pm More programming methods
- 4:00pm-5:00pm Hands-on session involving scatter plots, cluster analysis, and classification
- 6:00-8:00pm Dinner
- Invited key note speaker (B.M.?)
Day 4
Morning
- 8:00am-8:30am Associative Image Analysis - Part II (B.R.)
- 8:30am-9:30am Hands-on session involving cell classification, with FARSIGHT tools (team)
- 9:30am-10:00am Break
- 10:00am-11:00am Image registration fundamentals
- 11:00am - 12:00 Hands-on exercises involving registration and visualization of registration
- 12:00pm-1:00pm Working Lunch
- Participant presentations (15 mins each)
Afternoon
- 1:00pm - 1:30pm Fundamentals of time-lapse image analysis (change detection) (BR)
- 1:30pm - 2:00pm More programming methods
- 2:00pm-2:30pm Break
- 2:30pm - 3:30pm Hands-on session involving image pixel-level change detection (Team)
- 3:30pm - 4:00pm Cell and Organelle Tracking Methods
- 4:00pm - 5:00pm Hands-on session involving cell/organelle tracking
- 6:00-8:00pm Dinner
- Three participant presentations (15 min each)
Day 5
Morning
- 8:00am - 9:00am Associative Image Analysis - Part III
- 9:00am - 10:00am Advanced data analysis
- 10:00am-10:30am Break
- 10:30 - 12:00 Hands-on session involving FARSIGHT & Infovis tools
- 12:00 - 1:00 pm Working Lunch with a wrap-up presentation that summarizes the course, and points out what lies beyond.
Afternoon
- Participants may linger or depart when convenient
