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Does Organelle Shape Matter? Exploring Cell Shape through the Allen Cell Explorer and High-content Microscopy Datasets

By Carlos Christopher Goller1, Kaitlyn Casimo

North Carolina State University

The morphology and localization of structures inside the cell are often assumed to fit the ideal images found in biology textbooks. This interrupted case study using high-throughput microscopy data from the Allen Institute addresses this...

Listed in Teaching Materials | resource by group HITS

Version 2.0 - published on 13 Mar 2020 doi:10.25334/QJ2B-JW15 - cite this

Licensed under CC Attribution-NonCommercial 4.0 International according to these terms


Does Organelle Shape Matter? Exploring Cell Shape through the Allen Cell Explorer and High-content Microscopy Datasets

This interrupted case study suitable for upper-level undergraduate and graduate students uses a realistic scenario and the Allen Cell Explorer to guide students through the analysis of a novel data set produced by the Allen Institute that uses a high-throughput label-free approach to determine the localization and morphology of organelles. The case has several sections that engage students in use of the web resources from the Cell Explorer to analyze a scenario.

The student learning outcomes for this case are:

  1. Define the function of the endoplasmic reticulum and high-content microscopy 
  2. Explain in your own words the process the Allen Institute used to create a label-free prediction method for determining the location of 3D structures inside the cell, directly from transmitted light images.
  3. Access data from high-throughput discovery experiments from public databases
  4. Use the Cell Explorer 3D Cell Viewer tools to analyze image data to test your hypothesis
  5. Compare cell structures in the Allen 3D Cell Viewer.
  6. Evaluate the validity of this high-content imaging approach
  7. Design a future experiment to build on your findings


Cite this work

Researchers should cite this work as follows:


Draft 2. Tried Spring 2019 at NC State University.

Word version of lesson included. Use the Google Docs link to make your own editable copy of the activity. 


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