Growing Your Brain Outside Your Body; The Neurosphere Simulator

A brief introduction to neural cells

What are neural stem cells?

  1. dividing indefinitely
  2. giving rise to cells that go through the process of cellular differentiation

Where are neural stem cells found?

Diagram of the sub-ventricular zone
Diagram of the hippocampus

Why is neurogenesis so important?

What is a neurosphere assay?

What can we study with the neurosphere assay?

  1. How neural stem cell multipotency (ability to differentiate into different cell types) is affected by age
  2. Modeling how neurodegenerative diseases develop
  3. Screening neuroactive compounds — chemical agent made by a neuron that affects other neurons
  4. Testing the effects of pharmaceuticals on neural stem cells and differentiated neural cells
  5. Studying what factors affect how neural stem cells differentiate into the three main neural cell lineages: neurons, astrocytes, and oligodendrocytes

A simplified example of the protocol

1. Prepping the materials 🧴

2. Tissue dissection 🔪

3. Preparing the neurosphere 🧠

  • cell culture media — gel or liquid that provides the necessary amino acids, nutrients, and growth factors that regulate the cell cycle
  • trypsin — enzyme that breaks down the proteins that allow cells to stick together
  • trypsin-inhibitor — protein that neutralizes trypsin

4. Count cells 🔢

5. Add cells to a plate 🍽️

48-well plate


6. Examining the neurospheres 🔎

A cluster of several types of neural cells (one neurosphere)

The Neurosphere Simulator

What is the objective of the simulator?

How does the Neurosphere Simulator work?

Asymmetric Cell Divison

  1. Stem cells — indefinite proliferative potential
  2. Progenitor cells — limited proliferative potential
  3. Specialized cells — no proliferative potential
Figure 1 — types of neural cells interacting in the Neurosphere Simulator

Contact inhibition

Daughter position selection

Cell death

Example of two options when mitosis of a progenitor cell occurs. The left diagram shows both cells living while the right diagram shows the daughter cell dying


Example of how phagocytosis removes debris of dead cell, making room for new progenitor cell

My Findings

List of the variables in the simulation users can adjust

How does proliferative potential impact stem cell differentiation?

Legend showing what type of cells the colours on the graph and lattice correspond to
Data from trial 1, when proliferative potential was set to 7 (default setting)
Data from trial 2, when proliferative potential was set to 1 (lowest setting)

How does phagocytosis impact stem cell differentiation?

Data from trial 1, when clearance time was set to 5 (default setting)
Data from trial 3, when clearance time was set to 12 (highestsetting)


  • Data-driven — the simulation is based on data derived from scientific research done at the Laboratory of Neurobiology at Northeastern University
  • Virtual — due to the fact that it’s online, even people who don’t have access to laboratories where neurospheres are made can use it
  • Free — no financial barrier, unlike other resources
  • Interactive — there are several variables that the user can adjust, allowing them to see how the adjustments are connecting to stem cell differentiation
  • Intuitive design — the site itself is well-designed and easy to navigate
  • Built-in tutorial — the tutorial offered on the website concisely explains different concepts that the simulation models such as phagocytosis and contact inhibition, allowing you to have a clear idea of how to use the simulator
  • Visual component — unlike certain resources that solely represent data in dense sheets, the Neurosphere Simulator provides a graph and lattice-simulation side by side so that the user can easily see how a neurosphere would grow given the conditions they set





16-year-old activator at TKS figuring out stem cells and becoming less of a couch potato 🥔

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Aizah Malik

Aizah Malik

16-year-old activator at TKS figuring out stem cells and becoming less of a couch potato 🥔

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