Merge pull request #3 from royerlab/md-warning

Added extra instructions regarding markdown jupyter

tutorial/index.md

@@ -28,6 +28,12 @@ There are two goals with this tutorial:
 1. Introduce the participants to [ultrack package](https://github.com/royerlab/ultrack) and its capabilities.
 2. Show that there are other ways of segmentating and tracking cells rather than training by annotating thousands of cells and applying deep learning models. Pre-trained models and classical algorithms are our friends and can be used to solve many problems.
 
+## Notes
+
+```{warning}
+The notebooks are provided as Markdown files (`.md`) to open them as Jupyter Notebooks, you must right click on the file on your Jupyter interface and select `Open with` -> `Notebook`.
+```
+
 ## Instructors
 
 The instructors for this workshop are:

tutorial/tracking.md

@@ -358,6 +358,7 @@ for gamma in gammas:
 
 ```{code-cell} ipython3
 :tags: [remove-input]
+
 # printing the results
 pd.DataFrame(metrics).sort_values("TRA", ascending=False)
 ```
@@ -393,6 +394,7 @@ Once we have the combined contours and foreground, the process is the same as ev
 
 ```{code-cell} ipython3
 :tags: [remove-output]
+
 tracker.track(
    foreground=foreground,
    contours=contours,