Cellular Potts Modeling for Regeneration
Budget: $10 – $20 USD
We (a group of Grade 10 students) are conducting a research on a plant-based scaffold that we hope will foster true tissue regeneration, and I need a computational biologist who can turn our biological questions into a rigorous Cellular Potts Model. The single goal is to predict and visualise cell regeneration, adhesion, and growth on the scaffold, with particular emphasis on the rate of cell proliferation.
Here is what I can already put on the table: high-resolution microscopy image stacks of cells interacting with the scaffold over several days, plus a small dataset detailing the phytochemicals that remain embedded in the material. What I cannot provide is the coding expertise to translate these inputs into a CompuCell3D, Morpheus or similar CPM framework, calibrate it, and run the simulations.
I’m looking for someone who can:
• Build or adapt a CPM that reflects our experimental geometry and biochemical cues.
• Ingest the microscopy data for parameter tuning and validation.
• Generate clear plots and animations that track proliferation rates and spatial patterns over time.
• Walk me through the code structure so I can reproduce or extend the work later.
Acceptance of the final deliverable will be based on three items: a fully commented model script, a short technical report connecting simulation outputs to our observed proliferation curve, and a brief screen-share session where you demonstrate rerunning the model from scratch.
If this is your wheelhouse and you can start soon, let’s talk today.
Here is what I can already put on the table: high-resolution microscopy image stacks of cells interacting with the scaffold over several days, plus a small dataset detailing the phytochemicals that remain embedded in the material. What I cannot provide is the coding expertise to translate these inputs into a CompuCell3D, Morpheus or similar CPM framework, calibrate it, and run the simulations.
I’m looking for someone who can:
• Build or adapt a CPM that reflects our experimental geometry and biochemical cues.
• Ingest the microscopy data for parameter tuning and validation.
• Generate clear plots and animations that track proliferation rates and spatial patterns over time.
• Walk me through the code structure so I can reproduce or extend the work later.
Acceptance of the final deliverable will be based on three items: a fully commented model script, a short technical report connecting simulation outputs to our observed proliferation curve, and a brief screen-share session where you demonstrate rerunning the model from scratch.
If this is your wheelhouse and you can start soon, let’s talk today.