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Build a Pipeline to Segment Single-Cell Immunofluorescent Images 
Ali Al Abdullatif
Ali Al Abdullatif
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Build a Pipeline to Segment Single-Cell Immunofluorescent Images 

Design a high-throughput image analysis pipeline using Cell Profiler and ImageJ software.  

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Apply now
Wednesdays
 at
9:00
A.M.
 ET /
6:00
A.M.
PT
8 weeks, 2-3 hours per week
Intermediate
No experience required
No experience required
Some experience required
Degree and experience required

Description

Immunofluorescence is a widely used tool in the visualization of protein and biomolecules within fixed cultured cells (immunocytochemistry) or preserved and sectioned patient or animal tissue (immunohistochemistry). Fluorescent immunostaining is a reliable confirmation technique used across scientific disciplines both in academia and industry. However, without extremely expensive and proprietary software, analysis and interpretation of this data can be complicated and time-consuming. In this Build Project, you'll wear the hat of a scientist or engineer and build a pipeline capable of delivering high-throughput single cell data from immunofluorescent images. Under the supervision of an experienced Build Fellow, you'll design a segmentation workflow and analyze data. You'll become familiar with industry tools like Cell Profiler and ImageJ. All this will happen in an environment that simulates the operations of a real biotech team.

Session timeline

  • Applications open
    May 27, 2024
  • Application deadline
    June 23, 2024
  • Project start date
    Week of July 8, 2024
    Week of
    July 8, 2024
  • Project end date
    Week of

What you will learn

  • Conduct independent literature search
  • Build an image segmentation pipeline
  • Interrogate research for unresolved questions
  • Analyze and interpret data
Build Projects are 8-week experiences that operate on a rolling basis. Selected participants engage in weekly live workshops with a Build Fellow and 2-15 other students.

Project workshops

1
Introductions
2
The Basics of Immunofluorescence
3
Cell Profiler
4
Single Cell Segmentation
5
Experimental Data Set
6
Debugging
7
Data analysis
8
Final Session

Prerequisites

  • An interest in and basic understanding of molecular biology: functions of different cell types (Neurons, Microglia, Hepatocytes, Cardiomyocytes, etc.) and intracellular compartments (Nucleus, Cytoplasm, Lysosomes).  
  • Basic computer skills: you should be comfortable downloading new software and learning basic image manipulation techniques and protocol building.  

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About the expert
Ali Al Abdullatif
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Ali
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Neuroscience Research Scientist in a drug discovery and development role at CAMP4 Therapeutics. Neuroscience and psychology bachelor's degree from Boston University and master's degree in neuroengineering and biomedical engineering from Johns Hopkins University

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