Explicitly set dark mode images to avoid varnish image color inversion

CONTRIBUTING.md

@@ -65,24 +65,27 @@ fresh eyes are always welcome.
 ### What to Contribute (This Lesson)
 
 Any contributions are welcome, particularly ideas for how the existing content could be
-improved or updated, and/or errors that need to be corrected. Comments on existing issues 
+improved or updated, and/or errors that need to be corrected. Comments on existing issues
 and reviews of pull requests are similarly welcome.
 
 If you plan to submit a pull request, please open an issue
 (or comment on an existing thread) first to ensure that effort is not duplicated
 or spent making a change that will not be accepted by the Maintainers.
 
 #### Content / style guidelines
-- If you add an image / figure that was generated from Python code, please include this 
+
+- If you add an image / figure that was generated from Python code, please include this
   code in your PR under `episodes/fig/source`.
 
-- Use the terms in the table below, when referring to Python libraries within the lesson. 
-  The table gives two terms for each library: `Term for descriptive text` which should be 
-  used when discussing the library in plain English / full sentences and `Term for code` 
+- If you add a new image or figure, verify that it displays correctly in the lesson’s dark mode. A color-inversion filter is applied [by Varnish to all images by default in dark mode](https://github.com/carpentries/varnish/issues/181), which may cause some images to appear incorrectly or become unreadable. If your image is affected, include an additional version of the same image with a `-dark` suffix in its filename.
+
+- Use the terms in the table below, when referring to Python libraries within the lesson.
+  The table gives two terms for each library: `Term for descriptive text` which should be
+  used when discussing the library in plain English / full sentences and `Term for code`
   which should be used when referring to code (and within code).
 
    | Python library  | Term for descriptive text | Term for code  |
-   | :-------------  | :-------------            | :------------- | 
+   | :-------------  | :-------------            | :------------- |
    | [scikit-image](https://scikit-image.org/)  | scikit-image  | `skimage` |
    | [NumPy](https://numpy.org/)  | NumPy | `numpy` |
    | [Matplotlib](https://matplotlib.org/) | Matplotlib | `matplotlib` |
@@ -101,15 +104,15 @@ or spent making a change that will not be accepted by the Maintainers.
    rr, cc = ski.draw.rectangle(start=(357, 44), end=(740, 720))
    ```
 
-- For reading and writing images, use the [imageio](https://imageio.readthedocs.io/en/stable/index.html) 
+- For reading and writing images, use the [imageio](https://imageio.readthedocs.io/en/stable/index.html)
   library and avoid use of `skimage.io`. For example:
    ```python
    import imageio.v3 as iio
 
    chair = iio.imread(uri="data/chair.jpg")  # read an image
    iio.imwrite(uri="data/chair.tif", image=chair)  # write an image
    ```
-  
+
 - Comments providing an overall description of a code snippet should use triple quotes `"""`, e.g.,
    ```python
    """Python script to load a colour image in grayscale"""
@@ -138,7 +141,7 @@ Although most contributions will be welcome at this stage of the curriculum's de
 the time available to deliver the content in a training event is strictly limited
 and needs to be accounted for when considering the addition of any new content.
 If you want to suggest the addition of new content, especially whole new sections or episodes,
-please open an issue to discuss this with the Maintainers first and provide the following 
+please open an issue to discuss this with the Maintainers first and provide the following
 information alongside a summary of the content to be added:
 
 1. A suggested location for the new content.

episodes/03-skimage-images.md

@@ -191,7 +191,7 @@ Images may appear the same size in jupyter,
 but you can see the size difference by comparing the scales for each.
 You can also see the difference in file storage size on disk by
 hovering your mouse cursor over the original
-and the new files in the Jupyter file browser, using `ls -l` in your shell 
+and the new files in the Jupyter file browser, using `ls -l` in your shell
 (`dir` with Windows PowerShell), or viewing file sizes in the OS file browser if it is configured so.
 
 :::::::::::::::  solution
@@ -240,7 +240,7 @@ Suppose we are interested in this maize root cluster image.
 We want to be able to focus our program's attention on the roots themselves,
 while ignoring the black background.
 
-![](data/maize-root-cluster.jpg){alt='Root cluster image'}
+![](fig/maize-root-cluster.jpg){alt='Root cluster image'}
 
 Since the image is stored as an array of numbers,
 we can simply look through the array for pixel colour values that are
@@ -379,9 +379,9 @@ the low intensity pixels while changing the high intensity ones.
 
 The file `data/sudoku.png` is an RGB image of a sudoku puzzle:
 
-![](data/sudoku.png){alt='Su-Do-Ku puzzle'}
+![](fig/sudoku.png){alt='Su-Do-Ku puzzle'}
 
-Your task is to load the image in grayscale format and turn all of 
+Your task is to load the image in grayscale format and turn all of
 the bright pixels in the image to a
 light gray colour. In other words, mask the bright pixels that have
 a pixel value greater than, say, 192 and set their value to 192 (the
@@ -392,15 +392,15 @@ range 0-255 of an 8-bit pixel). The results should look like this:
 
 *Hint: the `cmap`, `vmin`, and `vmax` parameters of `matplotlib.pyplot.imshow`
 will be needed to display the modified image as desired. See the [Matplotlib
-documentation](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.imshow.html) 
+documentation](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.imshow.html)
 for more details on `cmap`, `vmin`, and `vmax`.*
 
 :::::::::::::::  solution
 
 ## Solution
 
-First, load the image file `data/sudoku.png` as a grayscale image. 
-Note we may want to create a copy of the image array to avoid modifying our original variable and 
+First, load the image file `data/sudoku.png` as a grayscale image.
+Note we may want to create a copy of the image array to avoid modifying our original variable and
 also because `imageio.v3.imread` sometimes returns a non-writeable image.
 
 ```python
@@ -465,11 +465,11 @@ Consider this image of a whiteboard, and suppose that we want to create a
 sub-image with just the portion that says "odd + even = odd," along with the
 red box that is drawn around the words.
 
-![](data/board.jpg){alt='Whiteboard image'}
+![](fig/board.jpg){alt='Whiteboard image'}
 
-Using `matplotlib.pyplot.imshow` 
+Using `matplotlib.pyplot.imshow`
 we can determine the coordinates of the corners of the area we wish to extract
-by hovering the mouse near the points of interest and noting the coordinates 
+by hovering the mouse near the points of interest and noting the coordinates
 (remember to run `%matplotlib widget` first if you haven't already).
 If we do that, we might settle on a rectangular
 area with an upper-left coordinate of *(135, 60)*

episodes/04-drawing.md

@@ -393,7 +393,7 @@ Copy that image to your computer, write some code to make a mask,
 and apply it to select the part of the image containing your object.
 For example, here is an image of a remote control:
 
-![](data/remote-control.jpg){alt='Remote control image'}
+![](fig/remote-control.jpg){alt='Remote control image'}
 
 And, here is the end result of a program masking out everything but the remote:
 
@@ -446,7 +446,7 @@ fig, ax = plt.subplots()
 ax.imshow(wellplate)
 ```
 
-![](data/wellplate-01.jpg){alt='96-well plate'}
+![](fig/wellplate-01.jpg){alt='96-well plate'}
 
 Suppose that we are interested in the colours of the solutions in each of the wells.
 We *do not* care about the colour of the rest of the image,

episodes/05-creating-histograms.md

@@ -52,7 +52,7 @@ and histograms are also quite handy as a preparatory step before performing
 We will start with grayscale images,
 and then move on to colour images.
 We will use this image of a plant seedling as an example:
-![](data/plant-seedling.jpg){alt='Plant seedling'}
+![](fig/plant-seedling.jpg){alt='Plant seedling'}
 
 Here we load the image in grayscale instead of full colour, and display it:
 

episodes/06-blurring.md

@@ -276,7 +276,7 @@ fig, ax = plt.subplots()
 ax.imshow(image)
 ```
 
-![](data/gaussian-original.png){alt='Original image'}
+![](fig/gaussian-original.png){alt='Original image'}
 
 Next, we apply the gaussian blur:
 
@@ -331,8 +331,8 @@ ax.imshow(blurred)
 
 ## Visualising Blurring
 
-Somebody said once "an image is worth a thousand words". 
-What is actually happening to the image pixels when we apply blurring may be 
+Somebody said once "an image is worth a thousand words".
+What is actually happening to the image pixels when we apply blurring may be
 difficult to grasp. Let's now visualise the effects of blurring from a different
 perspective.
 
@@ -430,18 +430,18 @@ but can be viewed by following the links in the captions.
 
 
 ![
-A 3D plot of pixel intensities across the whole Petri dish image before blurring. 
-[Explore how this plot was created with matplotlib](https://gist.github.com/chbrandt/63ba38142630a0586ba2a13eabedf94b). 
+A 3D plot of pixel intensities across the whole Petri dish image before blurring.
+[Explore how this plot was created with matplotlib](https://gist.github.com/chbrandt/63ba38142630a0586ba2a13eabedf94b).
 Image credit: [Carlos H Brandt](https://github.com/chbrandt/).
 ](fig/3D_petri_before_blurring.png){
 alt='3D surface plot showing pixel intensities across the whole example Petri dish image before blurring'
 }
 
 ![
-A 3D plot of pixel intensities after Gaussian blurring of the Petri dish image. 
-Note the 'smoothing' effect on the pixel intensities of the colonies in the image, 
-and the 'flattening' of the background noise at relatively low pixel intensities throughout the image. 
-[Explore how this plot was created with matplotlib](https://gist.github.com/chbrandt/63ba38142630a0586ba2a13eabedf94b). 
+A 3D plot of pixel intensities after Gaussian blurring of the Petri dish image.
+Note the 'smoothing' effect on the pixel intensities of the colonies in the image,
+and the 'flattening' of the background noise at relatively low pixel intensities throughout the image.
+[Explore how this plot was created with matplotlib](https://gist.github.com/chbrandt/63ba38142630a0586ba2a13eabedf94b).
 Image credit: [Carlos H Brandt](https://github.com/chbrandt/).
 ](fig/3D_petri_after_blurring.png){
 alt='3D surface plot illustrating the smoothing effect on pixel intensities across the whole example Petri dish image after blurring'

episodes/07-thresholding.md

@@ -68,7 +68,7 @@ fig, ax = plt.subplots()
 ax.imshow(shapes01)
 ```
 
-![](data/shapes-01.jpg){alt='Image with geometric shapes on white background' .image-with-shadow}
+![](fig/shapes-01.jpg){alt='Image with geometric shapes on white background' .image-with-shadow}
 
 Now suppose we want to select only the shapes from the image.
 In other words, we want to leave the pixels belonging to the shapes "on,"
@@ -214,7 +214,7 @@ ax.imshow(selection)
 Now, it is your turn to practice. Suppose we want to use simple thresholding
 to select only the coloured shapes (in this particular case we consider grayish to be a colour, too) from the image `data/shapes-02.jpg`:
 
-![](data/shapes-02.jpg){alt='Another image with geometric shapes on white background'}
+![](fig/shapes-02.jpg){alt='Another image with geometric shapes on white background'}
 
 First, plot the grayscale histogram as in the [Creating
 Histogram](05-creating-histograms.md) episode and
@@ -324,7 +324,7 @@ fig, ax = plt.subplots()
 ax.imshow(maize_roots)
 ```
 
-![](data/maize-root-cluster.jpg){alt='Image of a maize root'}
+![](fig/maize-root-cluster.jpg){alt='Image of a maize root'}
 
 We use Gaussian blur with a sigma of 1.0 to denoise the root image.
 Let us look at the grayscale histogram of the denoised image.
@@ -348,25 +348,25 @@ ax.set_xlim(0, 1.0)
 
 ![](fig/maize-root-cluster-histogram.png){alt='Grayscale histogram of the maize root image'}
 
-The histogram has a significant peak around 0.2 and then a broader "hill" around 0.6 followed by a 
+The histogram has a significant peak around 0.2 and then a broader "hill" around 0.6 followed by a
 smaller peak near 1.0. Looking at the grayscale image, we can identify the peak at 0.2 with the
 background and the broader peak with the foreground.
 Thus, this image is a good candidate for thresholding with Otsu's method.
 The mathematical details of how this works are complicated (see
 [the scikit-image documentation](https://scikit-image.org/docs/dev/api/skimage.filters.html#threshold-otsu)
 if you are interested),
 but the outcome is that Otsu's method finds a threshold value between the two peaks of a grayscale
-histogram which might correspond well to the foreground and background depending on the data and 
+histogram which might correspond well to the foreground and background depending on the data and
 application.
 
 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: instructor
 
-The histogram of the maize root image may prompt questions from learners about the interpretation 
-of the peaks and the broader region around 0.6. The focus here is on the separation of background 
-and foreground pixel values. We note that Otsu's method does not work well 
-for the image with the shapes used earlier in this episode, as the foreground pixel values are more 
+The histogram of the maize root image may prompt questions from learners about the interpretation
+of the peaks and the broader region around 0.6. The focus here is on the separation of background
+and foreground pixel values. We note that Otsu's method does not work well
+for the image with the shapes used earlier in this episode, as the foreground pixel values are more
 distributed. These examples could be augmented with a discussion of unimodal, bimodal, and multimodal
-histograms. While these points can lead to fruitful considerations, the text in this episode attempts 
+histograms. While these points can lead to fruitful considerations, the text in this episode attempts
 to reduce cognitive load and deliberately simplifies the discussion.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -636,10 +636,10 @@ def enhanced_root_mass(filename, sigma):
 
     # perform binary thresholding to mask the white label and circle
     binary_mask = blurred_image < 0.95
-    
+
     # perform automatic thresholding using only the pixels with value True in the binary mask
     t = ski.filters.threshold_otsu(blurred_image[binary_mask])
-    
+
     # update binary mask to identify pixels which are both less than 0.95 and greater than t
     binary_mask = (blurred_image < 0.95) & (blurred_image > t)
 
@@ -677,7 +677,7 @@ The `&` operator above means that we have defined a logical AND statement. This
 | False | True | False |
 | True | False | False |
 | True | True | True |
- 
+
 Knowing how to construct this kind of logical operation can be very helpful in image processing. The University of Minnesota Library's [guide to Boolean operators](https://libguides.umn.edu/BooleanOperators) is a good place to start if you want to learn more.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::

episodes/08-connected-components.md

@@ -27,7 +27,7 @@ we have covered dividing an image into foreground and background pixels.
 In the shapes example image,
 we considered the coloured shapes as foreground *objects* on a white background.
 
-![](data/shapes-01.jpg){alt='Original shapes image' .image-with-shadow}
+![](fig/shapes-01.jpg){alt='Original shapes image' .image-with-shadow}
 
 In thresholding we went from the original image to this version:
 
@@ -357,15 +357,15 @@ Those are really big numbers.
 From this available space we only use the range from `0` to `11`.
 When showing this image in the viewer,
 it may squeeze the complete range into 256 gray values.
-Therefore, the range of our numbers does not produce any visible variation. One way to rectify this 
+Therefore, the range of our numbers does not produce any visible variation. One way to rectify this
 is to explicitly specify the data range we want the colormap to cover:
 
 ```python
 fig, ax = plt.subplots()
 ax.imshow(labeled_image, vmin=np.min(labeled_image), vmax=np.max(labeled_image))
 ```
 
-Note this is the default behaviour for newer versions of `matplotlib.pyplot.imshow`. 
+Note this is the default behaviour for newer versions of `matplotlib.pyplot.imshow`.
 Alternatively we could convert the image to RGB and then display it.
 
 
@@ -376,7 +376,7 @@ Alternatively we could convert the image to RGB and then display it.
 ## Suppressing outputs in Jupyter Notebooks
 
 We just used `ax.set_axis_off();` to hide the axis from the image for a visually cleaner figure. The
-semicolon is added to supress the output(s) of the statement, in this [case](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.axis.html) 
+semicolon is added to supress the output(s) of the statement, in this [case](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.axis.html)
 the axis limits. This is specific to Jupyter Notebooks.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::

learners/edge-detection.md

@@ -128,7 +128,7 @@ We will execute the program on the `data/shapes-01.jpg` image,
 which we used before in
 [the *Thresholding* episode](../episodes/07-thresholding.md):
 
-![](data/shapes-01.jpg){alt='coloured shapes'}
+![](fig/shapes-01.jpg){alt='coloured shapes'}
 
 We are interested in finding the edges of the shapes in the image,
 and so the colours are not important.
@@ -225,7 +225,7 @@ based on the contents of the image(s) to be processed.
 Here is an image of some glass beads that we can use as
 input into a Canny edge detection program:
 
-![](data/beads.jpg){alt='Beads image'}
+![](fig/beads.jpg){alt='Beads image'}
 
 We could use the `code/edge-detection/CannyEdge.py` program above
 to find edges in this image.
@@ -394,7 +394,7 @@ Consider this image of a collection of maize seedlings,
 and suppose we wish to use simple fixed-level thresholding to
 mask out everything that is not part of one of the plants.
 
-![](data/maize-roots-grayscale.jpg){alt='Maize roots image'}
+![](fig/maize-roots-grayscale.jpg){alt='Maize roots image'}
 
 To perform the thresholding, we could first create a histogram,
 then examine it, and select an appropriate threshold value.