hotaru 4.0.1

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]

References

• Takekawa., T, et. al., HOTARU: Automatic sorting system for large scale calcium imaging data, bioRxiv, https://biorxiv.org/content/2022.04.05.487077 (2022).
• Takekawa., T, et. al., Automatic sorting system for large scale calcium imaging data, bioRxiv, https://www.biorxiv.org/content/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

Demonstration

hotaru sample --outdir mysample
cd mysample
hotaru config
# edit mysample/hotaru.ini if you need
hotaru trial
hotaru auto
hotaru mpeg --has-truth

• see mysample/hotaru/figure/

Sample Video

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