MouseLand · yarikoptic · Nov 17, 2025 · Nov 17, 2025 · Nov 17, 2025 · Nov 17, 2025
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,25 @@
+# Codespell configuration is within setup.cfg
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/README.md b/README.md
@@ -121,7 +121,7 @@ Next you can extract information from the videos like track keypoints, compute m
 
 ## I. Pose tracking
 
-<img src="https://raw.githubusercontent.com/MouseLand/facemap/main/figs/facemap.gif" width="100%" height="470" title="Tracker" alt="tracker" algin="middle" vspace = "10">
+<img src="https://raw.githubusercontent.com/MouseLand/facemap/main/figs/facemap.gif" width="100%" height="470" title="Tracker" alt="tracker" align="middle" vspace = "10">
 
 Facemap provides a trained network for tracking distinct keypoints on the mouse face from different camera views (some examples shown below). Check the `keypoints` box then click `process`. Next a bounding box will appear -- focus this on the face as shown below. Then the processed keypoints `*.h5` file will be saved in the output folder along with the corresponding metadata file `*.pkl`.
 
@@ -131,7 +131,7 @@ For more details on using the tracker, please refer to the [GUI Instructions](ht
 
 <p float="middle">
 <img src="https://raw.githubusercontent.com/MouseLand/facemap/main/figs/mouse_face1_keypoints.png"  width="310" height="290" title="View 1" alt="view1" align="left" vspace = "10" hspace="30" style="border: 0.5px solid white"  />
-<img src="https://raw.githubusercontent.com/MouseLand/facemap/main/figs/mouse_face0_keypoints.png" width="310" height="290" title="View 2" alt="view2" algin="right" vspace = "10" style="border: 0.5px solid white">
+<img src="https://raw.githubusercontent.com/MouseLand/facemap/main/figs/mouse_face0_keypoints.png" width="310" height="290" title="View 2" alt="view2" align="right" vspace = "10" style="border: 0.5px solid white">
 </p>
 
 ### 📢 User contributions 📹 📷

diff --git a/docs/conf.py b/docs/conf.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 # Configuration file for the Sphinx documentation builder.
 #

diff --git a/docs/installation.md b/docs/installation.md
@@ -19,7 +19,7 @@ If you are on Yosemite Mac OS, PyQt doesn't work, and you won't be able to insta
 
 The software has been heavily tested on Ubuntu 18.04, and less well tested on Windows 10 and Mac OS. Please post an issue if you have installation problems.
 
-### Pyhton dependencies
+### Python dependencies
 
 Facemap python relies on these awesome packages:
 - [pyqtgraph](http://pyqtgraph.org/)

diff --git a/docs/pose_tracking_gui_tutorial.md b/docs/pose_tracking_gui_tutorial.md
@@ -1,12 +1,12 @@
 # Pose tracking **(GUI)** :mouse:
 
-<img src="../figs/tracker.gif" width="100%" height="500" title="Tracker" alt="tracker" algin="middle" vspace = "10">
+<img src="../figs/tracker.gif" width="100%" height="500" title="Tracker" alt="tracker" align="middle" vspace = "10">
 
 The latest python version is integrated with Facemap network for tracking 14 distinct keypoints on mouse face and an additional point for tracking paw. The keypoints can be tracked from different camera views (some examples shown below). 
 
 <p float="middle">
 <img src="../figs/mouse_face1_keypoints.png"  width="310" height="290" title="View 1" alt="view1" align="left" vspace = "10" hspace="30" style="border: 0.5px solid white"  />
-<img src="../figs/mouse_face0_keypoints.png" width="310" height="290" title="View 2" alt="view2" algin="right" vspace = "10" style="border: 0.5px solid white">
+<img src="../figs/mouse_face0_keypoints.png" width="310" height="290" title="View 2" alt="view2" align="right" vspace = "10" style="border: 0.5px solid white">
 </p>
 
 ## Generate keypoints

diff --git a/docs/pose_tracking_gui_tutorial.rst b/docs/pose_tracking_gui_tutorial.rst
@@ -17,7 +17,7 @@ Follow the steps below to generate keypoints for your videos:
    -  For processing single video, select ``Load video``. Alternatively,
       for processing multiple videos, select ``Load multiple videos`` to
       select the folder containing the videos. (Note: Pose estimation
-      for multipl videos is only supported for videos recorded
+      for multiple videos is only supported for videos recorded
       simultaneously i.e. have the same time duration and frame rate).
 
    (Optional) Set output folder
@@ -38,7 +38,7 @@ Follow the steps below to generate keypoints for your videos:
    -  A dialog box for selecting a bounding box for the face will
       appear. Drag the red rectangle to select region of interest on the
       frame where the keypoints will be tracked. Please ensure that the
-      bouding box is focused on the face where all the keypoints will be
+      bounding box is focused on the face where all the keypoints will be
       visible. See example frames `here <https://github.com/MouseLand/facemap/blob/main/figs/mouse_views.png>`__. If a
       ‘Face (pose)’ ROI has already been added then this step will be
       skipped.

diff --git a/docs/svd_matlab_tutorial.md b/docs/svd_matlab_tutorial.md
@@ -97,7 +97,7 @@ You can draw areas to be included and excluded in the multivideo SVD (or single
 
 The motion energy is then computed from these non-red pixels.
 
-### Proccessed output
+### Processed output
 
 The GUIs create one file for all videos (saved in current folder), the processed mat file has name "videofile_proc.mat".
 

diff --git a/facemap/__init__.py b/facemap/__init__.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 name = "facemap"
 from facemap.version import version, version_str
diff --git a/facemap/__main__.py b/facemap/__main__.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import argparse
 import time

diff --git a/facemap/gui/cluster.py b/facemap/gui/cluster.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 

diff --git a/facemap/gui/gui.py b/facemap/gui/gui.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 import sys
@@ -836,7 +836,7 @@ def add_pose_model(self, pose_model_path=None):
             msg = QMessageBox()
             msg.setIcon(QMessageBox.Icon.Critical)
             msg.setText("Pose model not added. Error: " + str(e))
-            msg.setWindowTitle("Eror")
+            msg.setWindowTitle("Error")
             msg.setStandardButtons(QMessageBox.StandardButton.Ok)
             msg.exec_()
 
@@ -2250,7 +2250,7 @@ def update_ROI_vis_comboBox(self):
 
     def display_ROI(self):
         """
-        Plot selected ROI on visualizaiton window
+        Plot selected ROI on visualization window
         """
         self.roi_display_combobox.show()
         roi_request = self.roi_display_combobox.currentText()

diff --git a/facemap/gui/guiparts.py b/facemap/gui/guiparts.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import numpy as np
 import pyqtgraph as pg

diff --git a/facemap/gui/help_windows.py b/facemap/gui/help_windows.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 import typing

diff --git a/facemap/gui/io.py b/facemap/gui/io.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import glob
 import os

diff --git a/facemap/gui/menus.py b/facemap/gui/menus.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 from qtpy.QtWidgets import QAction
 from qtpy.QtGui import QGuiApplication

diff --git a/facemap/keypoints.py b/facemap/keypoints.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 

diff --git a/facemap/neural_prediction/keypoints_utils.py b/facemap/neural_prediction/keypoints_utils.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 

diff --git a/facemap/neural_prediction/neural_activity.py b/facemap/neural_prediction/neural_activity.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import numpy as np
 

diff --git a/facemap/neural_prediction/neural_model.py b/facemap/neural_prediction/neural_model.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import time
 from io import StringIO

diff --git a/facemap/neural_prediction/prediction_utils.py b/facemap/neural_prediction/prediction_utils.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 import time

diff --git a/facemap/pose/datasets.py b/facemap/pose/datasets.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 from glob import glob
@@ -254,7 +254,7 @@ def load_keypoints_h5(self):
         if len(annotation_files) == 0:
             raise ValueError("No .h5 files found in the directory")
 
-        # Landmarks dataframe concatentation
+        # Landmarks dataframe concatenation
         landmarks = pd.DataFrame()
         for f in annotation_files:
             df = pd.read_hdf(f)

diff --git a/facemap/pose/facemap_network.py b/facemap/pose/facemap_network.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Network ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 import numpy as np

diff --git a/facemap/pose/model_loader.py b/facemap/pose/model_loader.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 """
 Facemap model trained for generating pose estimates. Contains functions for: 

diff --git a/facemap/pose/model_training.py b/facemap/pose/model_training.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 ## Import packages
 import os

diff --git a/facemap/pose/pose.py b/facemap/pose/pose.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 import pickle

diff --git a/facemap/pose/pose_gui.py b/facemap/pose/pose_gui.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import numpy as np
 import pyqtgraph as pg

diff --git a/facemap/pose/pose_helper_functions.py b/facemap/pose/pose_helper_functions.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import random
 from platform import python_version

diff --git a/facemap/pose/refine_pose.py b/facemap/pose/refine_pose.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 import shutil

diff --git a/facemap/pose/transforms.py b/facemap/pose/transforms.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 """
 Facemap functions for: 
@@ -82,7 +82,7 @@ def randomize_bbox_coordinates(bbox, im_shape, random_factor_range=(0.1, 0.3)):
     im_shape: tuple of size (2,)
         image shape in order Ly, Lx
     random_factor_range: tuple of size (2,)
-        range of random factor to use for expaning bounding box
+        range of random factor to use for expanding bounding box
     Returns
     -------
     bbox: tuple of size (4,)

diff --git a/facemap/process.py b/facemap/process.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 import time
@@ -710,7 +710,7 @@ def run(
     Lybin, Lxbin, iinds = binned_inds(Ly, Lx, sbin)
     LYbin, LXbin, sybin, sxbin = utils.video_placement(Lybin, Lxbin)
 
-    # number of mot/mov ROIs
+    # number of mot/mov ROIs  # codespell:ignore
     nroi = 0
     if rois is not None:
         for r in rois:

diff --git a/facemap/pupil.py b/facemap/pupil.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import numpy as np
 from scipy.ndimage import gaussian_filter

diff --git a/facemap/roi.py b/facemap/roi.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import numpy as np
 import pyqtgraph as pg

diff --git a/facemap/running.py b/facemap/running.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 # outputs the dx, dy offsets between frames by registering frame N to frame
 # N-1. If the movement is larger than half the frame size, outputs NaN.

diff --git a/facemap/utils.py b/facemap/utils.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import cv2
 import h5py

diff --git a/facemap/version.py b/facemap/version.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 
 import sys

diff --git a/matlab/pupil/fitMVGaus.m b/matlab/pupil/fitMVGaus.m
@@ -1,10 +1,10 @@
 % fit 2D gaussian to cell with lam pixel weights
 function params = fitMVGaus(iy, ix, lam0, thres)
 
-% normalize pixel weigths
+% normalize pixel weights
 lam = lam0;
 
-% iteratively fit the Guassian, excluding outliers
+% iteratively fit the Gaussian, excluding outliers
 for k = 1:5
     lam     = lam / sum(lam);    
     mu      = [sum(lam.*iy) sum(lam.*ix)];    

diff --git a/paper/fig1.py b/paper/fig1.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import cv2
 import matplotlib

diff --git a/paper/fig3.py b/paper/fig3.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import matplotlib.pyplot as plt
 import torch

diff --git a/paper/fig4.py b/paper/fig4.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import matplotlib.pyplot as plt
 import torch

diff --git a/paper/fig_utils.py b/paper/fig_utils.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import string
 

diff --git a/paper/kpsproc.py b/paper/kpsproc.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 

diff --git a/paper/neuralpred.py b/paper/neuralpred.py
@@ -1,5 +1,5 @@
 """
-Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
+Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
 """
 import os
 import sys