https://github.com/bryanlimy/spikes2calcium

A simple Python tool to convert spike trains to calcium fluorescence-like traces.
https://github.com/bryanlimy/spikes2calcium

calcium-imaging spike-trains

Last synced: about 2 months ago
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A simple Python tool to convert spike trains to calcium fluorescence-like traces.

• Host: GitHub
• URL: https://github.com/bryanlimy/spikes2calcium
• Owner: bryanlimy
• License: mit
• Created: 2022-05-19T15:23:04.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2022-05-30T10:39:25.000Z (about 3 years ago)
• Last Synced: 2025-02-09T23:19:21.450Z (4 months ago)
• Topics: calcium-imaging, spike-trains
• Language: Python
• Homepage:
• Size: 288 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
## spikes2calcium

A simple Python tool to convert spike trains to calcium fluorescence-like traces.

---

### Files

- [`spikes2calcium.py`](spikes2calcium.py) - the main function to convert spike trains to calcium-like traces using the method described in [Grewe et. al. 2010](https://www.nature.com/articles/nmeth.1453) (codebase in MATLAB: [github.com/HelmchenLab/CalciumSim](https://github.com/HelmchenLab/CalciumSim)).

- [`utils.py`](utils.py) - includes plotting code and spike train generation code for the demo.

---

### Usage

```

import utils

from spikes2calcium import spikes2calcium

# generate spike trains from Poisson distribution

DURATION = 20  # duration of the simulation in s

NUM_NEURONS = 16  # number of neurons to simulate

FRAME_RATE = 24.0  # frame rate of the simulation

FIRING_RATE = 2.0  # firing rate in Hz

spike_trains = utils.generate_spike_trains(firing_rate=FIRING_RATE,

                                           duration=DURATION,

                                           num_neuorns=NUM_NEURONS,

                                           frame_rate=FRAME_RATE)

# convolve spike trains to calcium-like traces

traces = spikes2calcium(spike_trains=spike_trains, frame_rate=FRAME_RATE)

# plot the first 4 neurons

utils.plot_traces(traces=traces,

                  spike_trains=spike_trains,

                  frame_rate=FRAME_RATE,

                  filename='plots/traces.png',

                  show=False,

                  close=True)

```

### Example

![trace examples](plots/traces.png)

---

### Installation

- Package required: `numpy`, `matplotlib`