hotaru 4.0.0

High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse

HOTARU

High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse

Author

TAKEKAWA Takashi [e-mail]

Reference

• Takekawa., T, et. al., HOTARU: Automatic sorting system for large scale calcium imaging data, bioRxiv, preparing (2022).
• Takekawa., T, et. al., Automatic sorting system for large scale calcium imaging data, bioRxiv, https://doi.org/10.1101/215145 (2017).

Install

Require

• python >= 3.8
• tensorflow >= 2.8

Install Procedure (using venv)

• Create venv environment for hotaru
  • python3.x -m venv hotaru
• Activate hotaru environment
  • source hotaru/bin/activate
• Install hotaru
  • pip install hotaru

Usage

Config and Prepare

• Move to your workspace cd work
• Edit config file hotaru.ini

[DEFAULT]
imgs_path = imgs.tif
mask_type = 0.pad
hz = 20.0
tau_rise = 0.08
tau_fall = 0.16

[main]
tag = r20

[r20]
radius_max = 20.0

Check Cell Radius Stats

• Trial hotaru trial
• Check peaks stats [see hotaru/figure/r20_trial.pdf]
• Change radius_max if need

[DEFAULT]
imgs_path = imgs.tif
mask_type = 0.pad
hz = 20.0
tau_rise = 0.08
tau_fall = 0.16

[main]
tag = r10

[r10]
radius_max = 10.0

[r20]
radius_max = 20.0

Apply

• Run hotaru auto

Check Resutls

• see hotaru/figure/r10_curr.pdf and hotaru/output directory