From 0a283fe117c55a89278a3f35e6d761efe8c9bff3 Mon Sep 17 00:00:00 2001 From: carsen-stringer Date: Thu, 25 Apr 2024 07:18:11 -0600 Subject: [PATCH] Update README.md --- README.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 26af6af..b8532ed 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,6 @@ Rastermap runs in python 3.8+ and has a graphical user interface (GUI) for runni * [rastermap_interactive.ipynb](notebooks/rastermap_interactive.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MouseLand/rastermap/blob/main/notebooks/rastermap_interactive.ipynb) allows running Rastermap in an interactive way without a local installation * [tutorial.ipynb](notebooks/tutorial.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MouseLand/rastermap/blob/main/notebooks/tutorial.ipynb) is a guided tutorial for integrating rastermap and facemap to visualize behavioral representations. See the student/teacher versions [here](https://github.com/MouseLand/course-materials/tree/main/behavior_encoding). - All demo data available [here](https://osf.io/xn4cm/). Here is what the output looks like for a segment of a mesoscope recording in a mouse during spontaneous activity (3.2Hz sampling rate), compared to random neural sorting: @@ -42,7 +41,7 @@ Here is what the output looks like for a recording of wholebrain neural activity ### System requirements -Linux, Windows and Mac OS are supported for running the code. For running the graphical interface you will need a Mac OS later than Yosemite. At least 8GB of RAM is recommended to run the software. 16GB-32GB may be required for larger datasets. The software has been heavily tested on Windows 10 and Ubuntu 20.04 and less well-tested on Mac OS. Please open an [issue](https://github.com/MouseLand/rastermap/issues) if you have problems with installation. +Linux, Windows and Mac OS are supported for running the code. For running the graphical interface in Mac, you will need a Mac OS later than Yosemite. At least 8GB of RAM is recommended to run the software. 16GB-32GB may be required for larger datasets. The software has been heavily tested on Windows 10 and Ubuntu 20.04 and less well-tested on Mac OS. Please open an [issue](https://github.com/MouseLand/rastermap/issues) if you have problems with installation. ### Instructions @@ -137,12 +136,12 @@ spks = zscore(spks, axis=1) # fit rastermap model = Rastermap(n_PCs=200, n_clusters=100, - locality=0.75, time_lag_window=5).fit(spks) + locality=0.75, time_lag_window=5).fit(spks, compute_X_embedding=True) y = model.embedding # neurons x 1 isort = model.isort -# bin over neurons -X_embedding = zscore(utils.bin1d(spks[isort], bin_size=25, axis=0), axis=1) +# visualize binning over neurons +X_embedding = model.X_embedding # plot fig = plt.figure(figsize=(12,5))