Fluorescence Signal Analyzer for calcium imaging on user-defined neural structures.
Project description
FluoSA (Fluorescence Signal Analyzer)
FluoSA inputs *.LIF and *.tif files, detects user-defined neural structures, and quantifies the fluorescence signal changes (frame-wise fluorescence intensity and the dF/F0) in these structures.
The outputs of FluoSA include:
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An annotated video showing the detected neural structures:
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Spreadsheets storing frame-wise fluorescence intensity in each detected neural structure:
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Spreadsheets storing summary of fluorescence signal changes (dF/F0) in each detected neural structure:
Installation
1 Install FluoSA
python3 -m pip install FluoSA
2 Install CUDA toolkit v11.8
https://developer.nvidia.com/cuda-11-8-0-download-archive?target_os=Windows&target_arch=x86_64
3 Install Detectron2
python3 -m pip install 'git+https://github.com/facebookresearch/detectron2.git'
4 Install PyTorch 2.0.1
4.1 For Windows and Linux
4.1.1 If using GPU
python3 -m pip install torch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 --index-url https://download.pytorch.org/whl/cu118
4.1.2 CPU only
python3 -m pip install torch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 --index-url https://download.pytorch.org/whl/cpu
4.2 For Mac
python3 -m pip install torch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2
Usage
In your terminal / command prompt, type:
FluoSA
Then the user interface will be initiated:
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