11 cleanup of early lessons

config.yaml

@@ -68,8 +68,8 @@ contact: 'team@carpentries.org'
 episodes:
 - imaging-software.Rmd
 - getting-started-with-napari.Rmd
-- napari-notebook.Rmd
 - what-is-an-image.Rmd
+- napari-notebook.Rmd
 - instance-segmentation-classic.Rmd
 
 # Information for Learners

episodes/getting-started-with-napari.Rmd

@@ -114,7 +114,8 @@ various aspects of the Napari viewer:
 https://raw.githubusercontent.com/napari/napari/main/src/napari/resources/icons/console.svg
 ){alt="A screenshot of Napari's console button" height='30px'}
 
-This button opens Napari's built-in python console.
+This button opens Napari's built-in python console, where we can enter in
+Python commands to interact with the imaging data. 
 
 ### 2D/3D ![](
 https://raw.githubusercontent.com/napari/napari/main/src/napari/resources/icons/2D.svg

episodes/instance-segmentation-classic.Rmd

@@ -82,6 +82,9 @@ image = viewer.layers["nuclei"].data
 # Smooth the image
 blurred = gaussian(image, sigma=3)
 
+# Add the image to the viewer
+viewer.add_images(blurred)
+
 # Compute a threshold
 threshold = threshold_otsu(blurred)
 

episodes/what-is-an-image.Rmd

@@ -86,7 +86,30 @@ We've seen that images are made of individual units called pixels that have
 specific values - but how is an image really represented in the computer? Let's 
 dig deeper into Napari's `Image` layers...
 
-In our notebook, let's look at the human mitosis image more closely - copy the text in the 
+First, open Napari's built-in Python console by pressing the console button ![](
+https://raw.githubusercontent.com/napari/napari/main/src/napari/resources/icons/console.svg
+){alt="A screenshot of Napari's console button" height='30px'}. 
+Note this can take a few seconds to open, so give it some time:
+
+![](fig/console.png){alt="A screenshot of Napari's console"}
+
+:::::::::::::::::::::::::::::::::::::: callout
+
+### Console readability
+
+You can increase the font size in the console by clicking inside it, then 
+pressing <kbd>Ctrl</kbd> and <kbd>+</kbd> together. The font size can also be 
+decreased with <kbd>Ctrl</kbd> and <kbd>-</kbd> together.
+
+Note that you can also pop the console out into its own window by clicking the 
+small ![](
+https://raw.githubusercontent.com/napari/napari/main/src/napari/resources/icons/pop_out.svg
+){alt="A screenshot of Napari's float panel button" height='30px'} 
+icon on the left side.
+
+::::::::::::::::::::::::::::::::::::::::::::::::
+
+Let's look at the human mitosis image more closely - copy the text in the 
 'Python' cell below into Napari's console and then press the <kbd>Enter</kbd> 
 key. You should see it returns text that matches the 'Output' cell below in 
 response.
@@ -97,8 +120,9 @@ here we access the top (first) layer with `viewer.layers[0]`. Then, to access
 the actual image data stored in that layer, we retrieve it with `.data`:
 
 :::::::::::::::::::::::: instructor
-# By number of by label
-SHow that the layer can also be accessed via the name of the layer
+# Working in the console
+Instead of the notebook, use the console. And by sow that the layer can also 
+be accessed via the name of the layer
 ::::::::::::::::::::::::
 
 ```python

learners/setup.md

@@ -8,6 +8,17 @@ All images will be pre-loaded examples that are already part of Napari.
 Provided Napari software is loaded correctly, you are all set!
 
 ## Software Setup
+
+### Opening a Terminal
+
+You will need a terminal to run some of the setup instructions and commands
+for this workshop: 
+
+ - **Windows (if you used Miniforge)**: Click Start > Search for Miniforge Prompt > Click to Open
+ - **Windows (if you used Anaconda)**: Click Start > Search for Anaconda Prompt > Click to Open
+ - **macOS**: Launchpad > Other Application > Terminal
+ - **Linux**: Open a terminal window
+
 ### Install uv
 
 `uv` is a Python package manager and environment tool. Use the