benchmarking challenge for finding neurons in imaging data
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
client minor fixes for db updates Jul 2, 2018
server minor fixes for db updates Jul 2, 2018
.gitignore refactoring Mar 22, 2016
README.md Update README.md Jul 16, 2016
package.json add schema validation and debug logging Mar 28, 2016

README.md

neurofinder Join the chat at https://gitter.im/codeneuro/neurofinder

benchmarking challenge for finding neurons in calcium imaging data.

Calcium imaging is a widely used techniqe in modern neuroscience for measuring the activity of large populations of neurons. Identifying individual neurons in these images remains a challenge, and most approaches still rely on manual inspection or annotation. We have assembled a collection of datasets with ground truth labels, and made a small web app for researchers to submit results and compare algorithms.

This repo contains the code for the web app (for displaying and submitting results) and the server (for retrieving and updating results from a database). This document describes how to download the data, develop algoritms in your favorite computing environment, and submit your results for evaluation!

For more info, check out the following repositories:

step (1) download and develop

  1. Browse the list of datasets below.
  2. Download one or more of them.
  3. Use the example scripts to learn how to load the data (examples in python, javascript, and matlab).
  4. Develop and refine your algorithm.

During development, you might want to use the neurofinder python module to evaluate the performance of your algorithm on the training data. It computes the same metrics that will be used to evaluate your algorithm. If you are working in another language, you can look at that repository for a full explanation of the metrics, and see the source code (it's pretty simple!)

step (2) submit your algorithm

  1. Run your algorithm on all the testing datasets.
  2. Go to the neurofinder website.
  3. Click the submit tab and upload your results file!

submission format

Your results should be formatted as a single JSON file with the coordinates of all identified neurons for all testing datasets, in the following format:

[
  {
    "dataset": "00.00.test",
    "regions": [{"coordinates": [[x, y], [x, y], ...]}, {"coordinates": [[x, y], [x, y], ...]}, ...]
  },
  {
    "dataset": "00.01.test",
    "regions": [{"coordinates": [[x, y], [x, y], ...]}, {"coordinates": [[x, y], [x, y], ...]}, ...]
  },
  ...
]

If you are working in python, you can generate this file by storing your results in a list of dictionaries and writing it to JSON:

import json
results = [
  {'dataset': '00.00.test', 'regions': [{'coordinates': [[0, 1], [2, 3]]}]},
  {'dataset': '00.01.test', 'regions': [{'coordinates': [[0, 1], [2, 3]]}]},
]
with open('results.json', 'w') as f:
  f.write(json.dumps(results))

If you are working in matlab, get jsonlab then generate and save a nested struct:

results = [
  struct('dataset', '00.00.test', 'regions', struct('coordinates', [[0, 1]; [2, 3]])),
  struct('dataset', '00.01.test', 'regions', struct('coordinates', [[0, 1]; [2, 3]]))
]
savejson('', results, 'results.json')

If you are working in javascript, just build and write the object:

results = [
  {dataset: '00.00.test', regions: [{coordinates: [[0, 1], [2, 3]]}]},
  {dataset: '00.01.test', regions: [{coordinates: [[0, 1], [2, 3]]}]},
]
require('fs').writeFile('results.json', JSON.stringify(results))

datasets

Datasets have been generously provided by the following individuals and labs:

  • Simon Peron, Nicholas Sofroniew, & Karel Svoboda / Janelia Research Campus : 00, 02
  • Adam Packer, Lloyd Russell & Michael Häusser / UCL : 01
  • Jeff Zaremba, Patrick Kaifosh & Attila Losonczy / Columbia : 03
  • Selmaan Chettih, Matthias Minderer, Chris Harvey / Harvard : 04

All datasets are hosted on Amazon S3, and direct links to zipped downloads are below.

Each dataset includes

  • raw image data as a collection of 2D TIFF files that represent a single imaging plane over time
  • example scripts for loading data in both python, javascript, and matlab

The training data additionally includes the coordinates of identified neurons (the "ground truth") as JSON. Depending on the dataset, these ground truth labels are based on a separate anatomical nuclear marker and/or hand annotations from the dataset providers.

training data

neurofinder.00.00 neurofinder.00.01 neurofinder.00.02 neurofinder.00.03 neurofinder.00.04 neurofinder.00.05 neurofinder.00.06 neurofinder.00.07 neurofinder.00.08 neurofinder.00.09 neurofinder.00.10 neurofinder.00.11 neurofinder.01.00 neurofinder.01.01 neurofinder.02.00 neurofinder.02.01 neurofinder.03.00 neurofinder.04.00 neurofinder.04.01

testing data

neurofinder.00.00.test neurofinder.00.01.test neurofinder.01.00.test neurofinder.01.01.test neurofinder.02.00.test neurofinder.02.01.test neurofinder.03.00.test neurofinder.04.00.test neurofinder.04.01.test

web app

To run the web app in development, clone this repo, then call

npm install
npm start

Which will start the server and live bundle the static assets.

To run in production, bundle the static assets using npm run build then start the server using npm run serve.

You need to specify a mongo database inside server/config.js, and also set the environmental variables MONGO_USER and MONGO_PASSWORD. A script for fetching datasets is included in server/fetch.js, and also requires that AWS_ACCESS_KEY_ID, and AWS_SECRET_ACCESS_KEY, because the data is fetched from S3.