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Small internal package for post-selection of Glutmate/Calcium signal responses.
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You will need Anaconda to be installed. If Anaconda is installed, open the "Anaconda Prompt" (Windows) or a terminal (Linux + Mac).
Create a conda enviorment:
conda create -n synapse_selector python=3.10 pip
conda activate synapse_selector
Install synapse selector:
pip install synapse_selector
Alternatively, you can also clone this repository and install it from there
git clone https://github.com/s-weissbach/synapse_selector.git
cd synapse_selector
pip install -e .
The mean traces should be stored in a .csv
or an excel file .xls
, .xlsx
. Ensure that the mean traces are organized with one trace per column. You can have columns with meta information (e.g. Time) that will be carried over to the output files.
Example input file
Time (ms) | Trace 1 | Trace 2 | (...) |
---|---|---|---|
0 | 23.5 | 18.7 | (...) |
1 | 25.1 | 20.3 | (...) |
2 | 22.8 | 17.6 | (...) |
3 | 21.4 | 19.2 | (...) |
4 | (...) | (...) | (...) |
[!Tip] Meta columns won't be included for analysis, but will be carried over to the output files.
To run Synapse Selector, follow these steps:
conda activate synapse_selector
python -m synapse_selector
To access the settings, press the settings symbol in the top icon bar. The settings are organized in the Tabs
General
, Detection
, Threshold Settings
, and Stimulation
.
In the general settings section, you can configure the following options:
[!NOTE] Rolling window z-normalization will be applied for detection.
Configure the detection settings according to your analysis preferences:
[!NOTE] Threshold is calculated witht the formula: $$\text{threshold} = (\text{multiplier} * std_{baseline}) + mean_{baseline}$$
[!IMPORTANT] When entering stimulation frames manually, separate the frames by commas without spaces.
Command | Button | Shortcut | Description |
---|---|---|---|
Open File | Ctrl + O | Open a file | |
Save File | Ctrl + S | Save all traces up to this point and discard the rest | |
Settings | S | Open the settings | |
Back | B | Go one trace back | |
Discard | Q | Discard trace from analysis | |
Accept | E | Accept trace and keep for analysis | |
Modify Responses | W | Add or remove responses |
Open a File pressing the open button in the top bar.
Modify responses pressing the modify response button in the top bar
Accept or Discard a trace
Change certantiy threshold (only when using ML-based detection):
Save and skip rest: press the save button in the top bar. All remaining traces of the file will be discarded.
See the Synapse Selector Detect for detailed tutorial on how to train a custom model.
[!Tip] You can share your model with the community - submit it to Synapse Selector Modelzoo.GitHub - s-weissbach/synapse_selector_modelzoo.
FAQs
Small internal package for post-selection of Glutmate/Calcium signal responses.
We found that synapse-selector demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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