Paul Brodersen paulbrodersen
paulbrodersen
/ synaptic_inputs.py
Last active
December 4, 2024 16:04
Find synaptic inputs in voltage or current traces
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| #!/usr/bin/env python3 | |
| # -*- coding: utf-8 -*- | |
| """This program identifies synaptic inputs in voltage and current | |
| electrophysiological recordings. | |
| Copyright (C) 2024 Gemma Gothard, Paul Brodersen | |
| This program is free software: you can redistribute it and/or modify | |
| it under the terms of the GNU General Public License as published by | |
| the Free Software Foundation, either version 3 of the License, or |
paulbrodersen
/ dynamic_opacity.py
Created
August 14, 2024 11:51
Create a scatter plot with dynamic opacity.
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| """Scatter plots with dynamic opacities. | |
| Inspired by: | |
| https://observablehq.com/@rreusser/selecting-the-right-opacity-for-2d-point-clouds. | |
| Copyright (C) 2024 by Paul Brodersen. | |
| This program is free software: you can redistribute it and/or modify | |
| it under the terms of the GNU General Public License as published by |
paulbrodersen
/ extract_sioyek_highlights.py
Created
June 20, 2024 12:23
Extract Sioyek highlights to a text file.
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| """Export highlights made with the Sioyek PDF viewer | |
| (https://github.com/ahrm/sioyek/) as a text document. | |
| Copyright (C) 2024 by Paul Brodersen. | |
| This program is free software: you can redistribute it and/or modify | |
| it under the terms of the GNU General Public License as published by | |
| the Free Software Foundation, either version 3 of the License, or (at | |
| your option) any later version. This program is distributed in the | |
| hope that it will be useful, but WITHOUT ANY WARRANTY; without even |
paulbrodersen
/ svg2tiff
Created
January 15, 2024 11:43
— forked from matsen/svg2tiff
A script to convert SVG to a TIFF acceptable to PLOS
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| #!/bin/sh | |
| # Convert all arguments (assumed SVG) to a TIFF acceptable to PLOS | |
| # Requires Inkscape and ImageMagick 6.8 (doesn't work with 6.6.9) | |
| for i in $@; do | |
| BN=$(basename $i .svg) | |
| inkscape --without-gui --export-png="$BN.png" --export-dpi 300 $i | |
| convert -compress LZW -alpha remove $BN.png $BN.tiff | |
| mogrify -alpha off $BN.tiff |
paulbrodersen
/ burman_et_al_2023_neuropixel_data_analysis.py
Last active
June 12, 2023 15:49
Code to reproduce analysis of Claar et al (2023) neuropixel data in Burman et al. (2023)
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| #!/usr/bin/env python | |
| # -*- coding: utf-8 -* | |
| """ Extract data from Claar et al. (2023) & compute for each unit its | |
| - evoked firing rate, | |
| - peri-stimulus histogram entropy, and | |
| - synchrony. | |
| The dataset is available at: |
paulbrodersen
/ burman_et_al_2023_neuronal_network_simulation.py
Last active
June 12, 2023 15:48
Code to reproduce neuronal network simulations in Burman et al. (2023).
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| #!/usr/bin/env python | |
| # -*- coding: utf-8 -* | |
| """Simulate a LIF neuronal network with variable EGABA and structured inputs. | |
| Copyright (C) 2023 by Paul Brodersen. | |
| This program is free software: you can redistribute it and/or modify | |
| it under the terms of the GNU General Public License as published by | |
| the Free Software Foundation, either version 3 of the License, or (at |
paulbrodersen
/ alfonsa_2020_neuronal_network_simulation.py
Last active
January 8, 2024 11:59
Code to run neuronal network simulation in Alfonsa et al (2020)
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| #!/usr/bin/env python | |
| # -*- coding: utf-8 -* | |
| """ | |
| Determine the effect of changes in the GABA reversal potential in | |
| pyramidal neurons on their ability to synchronize. | |
| Copyright (C) 2020 by Paul Brodersen. | |
| This program is free software: you can redistribute it and/or modify |