Small internal package for post-selection of Glutmate/Calcium signal responses.
Project description
Trace Selector
Table of Contents
Overview
A small GUI programm to ease the post-selection of average traces of functional recordings. The user can edit automatically detected response events (thresholding, ML-detecition, or both). Trace Selector
will automatically compute various commonly used metrics (e.g. failure rate, paired-pulse ratio)
Installation
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 trace_selector python=3.10 pip conda activate trace_selector
-
Install trace selector:
pip install trace_selector
Build from source
Alternatively, you can also clone this repository and install it from there
git clone https://github.com/s-weissbach/trace_selector.git
cd trace_selector
pip install -e .
Getting Started
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.
Run Trace Selector
To run Trace Selector, follow these steps:
-
conda activate trace_selector
- Launch the Trace Selector using the following command:
python -m trace_selector
Adapt the Settings
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
.
General
In the general settings section, you can configure the following options:
- Set Output Path: Specify the directory where you want the output files to be saved.
- Export as XLSX: Choose whether to export the results in XLSX format, otherwise .csv files will be created.
- Add/Remove Meta Columns: Customize the meta columns based on your requirements.
Detection
[!NOTE] Rolling window z-normalization will be applied for detection.
Configure the detection settings according to your analysis preferences:
- Selection Methods: Choose between ML-based and Thresholding.
- Deep Learning Model: If ML-based selection is chosen, specify the deep learning model specific for the sensor you used.
- Time Window for Tau Computation: Set the time window for tau computation, which determines the decay estimate.
- Show Normalized Trace (Toggle): Toggle this option to display z-normalized traces in the output.
- Compute PPR (Toggle): If stimulation was used, enable this option to compute the paired pulse ratio (PPR).
Threshold Settings
- Baseline Start: Specify the start point of the baseline for threshold calculation.
- Baseline Stop: Define the stop point of the baseline for threshold calculation.
- Threshold Multiplier: Set the multiplier used in the
[!NOTE] Threshold is calculated witht the formula: $$\text{threshold} = (\text{multiplier} * std_{baseline}) + mean_{baseline}$$
Stimulation
- Enable Stimulation (Toggle): Toggle this option when you used stimulation in this recording.
- Start Frame for Stimulation: Specify the starting frame for stimulation. Stimulation frames will be infered automatically.
- Step Size for Stimulation: Set the step size for stimulation. Stimulation frames will be infered automatically.
- Patience: Define the duration for which a response should be counted as a valid response to the stimulation.
- Use Manual Stimulation Frames: Input stimulation frames manually
[!IMPORTANT] When entering stimulation frames manually, separate the frames by commas without spaces.
Usage
Shortcuts and brief overview
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 |
Detailed explanation
-
Open a File pressing the open button
in the top bar.
- Trace Selector will visualize the first column of the file that is not a meta column.
- All detected responses will be annotated.
- If specified in the settings, a horizontal, red dashed line will be shown
-
Modify responses pressing the modify response button
in the top bar
- A window with all detected responses will be opened
- Deselect false-positive responses
- Add false-negative responses
-
Accept or Discard a trace
- To accept a trace and subsequently include it in the analysis:
- To discard a trace from analysis:
- To accept a trace and subsequently include it in the analysis:
-
Change certantiy threshold (only when using ML-based detection):
- Use the slider at the bottom to adjust the certantiy threshold used in the model. A lower threshold will lead to more detections, possibly, to more false-positives.
-
Save and skip rest: press the save button
in the top bar. All remaining traces of the file will be discarded.
Train a custom Model
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 Trace Selector Modelzoo.GitHub - s-weissbach/synapse_selector_modelzoo.
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