Cell Counter

Counting circles, how hard can it get?

Cell Counter

This open source project is designed to help researchers automate computer vision tasks; it’s built to reduce as much groundwork as possible so they can focus on their tasks. To explain it simply Cell-Counter is a generic project that wraps computer vision utilities and lets you use them as you see fit in already existing algorithms or new ones, its free to use and easy to expand upon.

As for the specifics Cell-Counter is built on top of a very known library ImageJ. This library lacks some practical features such as apply an algorithm to multiple files, so the idea is using all the potential in ImageJ but still be flexible. Cell-Counter can be used to integrate computer vision into any workflow or to simply obtain local results, the core is designed to be extensible, flexible and it's fully tested for better maintainability.

To illustrate how it can be used the first algorithm published was the Cell-Counter algorithm that lets you count cells given a folder and some configurations, the output of the execution is a CVS file with all the data of the cells on each image, and an output image. Up next you will see each one of the steps taken by the algorithm:

  • Start
  • Color to grayscale
  • Filter out noise
  • Dynamic thresholder
  • Erode
  • Watershed
  • Result

I do really think developers should be more involved in the research field, sadly research isn't known for huge budgets and can't simply invest in developers as much as the companies. I think automating is the way otherwise we simply waste time.

This project was intended to help others, it would mean the world to me if it could help anyone.