cellcanvas / cellcanvas/cellcanvas-prototype

Goals and scope for CellCanvas

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#24 2 comments 1 reaction 0 assignees View on GitHub
Dominant language
Python
Stars
12
Forks
5
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Description

I am creating this issue to discuss our goals and scope for CellCanvas.

From my perspective, CellCanvas is a software library for building geometric models of intracellular architecture. These models can be used for quantifying and comparing morphology as well as for input into simulations.

The core library contains:
- geometric models for all key intracellular components. This includes meshes (e.g., for membranes), networks of splines (e.g., for filaments), and particles (both position and orientation).
- data models for defining collections of the geometric models
- algorithms for extracting the models from imaging data (e.g., segmentation, pixel embeddings)
- a graphical user interface for extracting and building the models from images

Non-goals:
- provide state-of-the-art performance for all computer vision tasks. I think we should provide solid implementations of some core tasks, but also make it easy for users to import results from other algorithms
- perform simulations. I think we should be able to export the geometries to simulation software easily, but I don't think we need to have any sort of simulation engine in the core.

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Research direction

No files, tests, or entry points are named. Start by reading the issue discussion and repository overview to understand the proposed library boundaries; the issue does not define a concrete change or a verifiable done condition.

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Assessment

Tech stack
python
Domain
computer-vision, desktop, machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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