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@@ -4,17 +4,17 @@ Custom code to compute **centripetal propagation** patterns (delay maps) from **
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<p align="center"><img src="https://github.com/HelmchenLabSoftware/Centripetal_propagation_astrocytes/blob/main/Github%20centripetal%20propagation.png" width="65%"></p>
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This image illustrates mean fluorescence (left) and computed delay maps (right). Delay maps are organized such that positive delays are close to astrocytic somata and negative delays far from somata (middle). These delay maps illustrate that astrocytic calcium signals propagate from distal processes to somatic compartments for individual astrocytes.
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This image shows mean fluorescence (left) and computed delay maps (right). Delays are positive close to astrocytic somata and negative far from somata (middle). These delay maps illustrate that astrocytic calcium signals propagate from distal processes to somatic compartments for individual astrocytes.
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### How the algorithm works
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The code computes the delay with respect to a reference time trace for each pixel of a 3D movie. This enables to extract typical spatio-temporal delays with respect to a mean time trace across the movie. It works best for either long or relatively noise-free movies. The details of the algorithm are described in Fig. 6 and the associated supplementary figures in **[this preprint](https://www.biorxiv.org/content/10.1101/2022.08.16.504030v1.full)**.
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The code computes the delay with respect to a reference time trace for each pixel of a 3D movie. The reference time trace is generated by averaging across the entire field-of-view. This enables to extract typical spatio-temporal delays with respect to a mean time trace across the movie. It works best for either long or relatively noise-free movies. The details of the algorithm are described in Fig. 6 and the associated supplementary figures in **[this preprint](https://www.biorxiv.org/content/10.1101/2022.08.16.504030v1.full)**.
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### How to use the algorithm
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- The code includes extensive comments and should be mostly self-explanatory.
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- The code is not optimized for performance in order to keep it as simple as possible.
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- The code is not optimized for performance, in order to keep it as simple as possible. Parallelization is implemented for the Matlab but not for the Python version.
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- The scripts `Demo_analysis_Matlab.m` and `Demo_analysis_Python.py` use a calcium imaging recording as a tif-file and produce a delay map as shown here.
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### How to cite this work
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If you use these scripts in its original or in a modified version, please cite the following publication as reference:
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If you use these scripts in its original or in a modified version, please cite the following publication as reference. An updated version of the preprint will be made available in Summer 2023:
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> Rupprecht, P., Lewis, C. M., & Helmchen, F. *Centripetal integration of past events by hippocampal astrocytes.* bioRxiv, 2022-08 (2022). [https://www.biorxiv.org/content/10.1101/2022.08.16.504030v1](https://www.biorxiv.org/content/10.1101/2022.08.16.504030v1)
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