markdown source builds

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Source  : 838a0c8
Branch  : main
Author  : Stephen Thompson <s.thompson@ucl.ac.uk>
Time    : 2026-06-08 15:06:02 +0000
Message : Consistent layer numbering for filetypes and metadata (#126)

* Consistent layer numberng

* Update episodes/filetypes-and-metadata.md

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>

* Update episodes/filetypes-and-metadata.md

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>

* Update episodes/filetypes-and-metadata.md

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>

---------

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>

Author: actions-user

filetypes-and-metadata.md

@@ -325,18 +325,18 @@ image_layer.scale = (0.35, 0.2047619, 0.2047619)
 
 ## Pixel size / scale
 
-Copy and paste the following into Napari's console to get `image_layer_1`, 
-`image_layer_2` and `image_layer_3` of the yeast image:
+Copy and paste the following into Napari's console to get `image_layer_0`,
+`image_layer_1` and `image_layer_2` of the yeast image:
 
 ```python
-image_layer_1 = viewer.layers[0]
-image_layer_2 = viewer.layers[1]
-image_layer_3 = viewer.layers[2]
+image_layer_0 = viewer.layers[0]
+image_layer_1 = viewer.layers[1]
+image_layer_2 = viewer.layers[2]
 ```
 
 1. Check the `.scale` of each layer - are they the same?
-2. Set the scale of layer 3 to (0.35, 0.4, 0.4) - what changes in the viewer?
-3. Set the scale of layer 3 to (0.35, 0.4, 0.2047619) - what changes in the 
+2. Set the scale of `image_layer_2` to (0.35, 0.4, 0.4) - what changes in the viewer?
+3. Set the scale of `image_layer_2` to (0.35, 0.4, 0.2047619) - what changes in the 
 viewer?
 4. Set the scale of all layers so they are half as wide and half as tall as 
 their original size in the viewer
@@ -351,9 +351,9 @@ their original size in the viewer
 All layers have the same scale
 
 ```python
+print(image_layer_0.scale)
 print(image_layer_1.scale)
 print(image_layer_2.scale)
-print(image_layer_3.scale)
 ```
 ```output
 [0.35 0.2047619 0.2047619]
@@ -363,40 +363,40 @@ print(image_layer_3.scale)
 
 ### 2
 
-![](fig/yeast-exercise-2.png){alt="Yeast image shown in Napari with layer 3 
+![](fig/yeast-exercise-2.png){alt="Yeast image shown in Napari with layer 2
 twice as big in y and x"}
 
 ```python
-image_layer_3.scale = (0.35, 0.4, 0.4)
+image_layer_2.scale = (0.35, 0.4, 0.4)
 ```
-You should see that layer 3 becomes about twice as wide and twice as tall as the 
-other layers. This is because we set the pixel size in y and x (which used to 
+You should see that layer 2 becomes about twice as wide and twice as tall as the
+other layers. This is because we set the pixel size in y and x (which used to
 be 0.2047619μm) to about twice its original value (now 0.4μm).
 
 ### 3
 
-![](fig/yeast-exercise-3.png){alt="Yeast image shown in Napari with layer 3 
+![](fig/yeast-exercise-3.png){alt="Yeast image shown in Napari with layer 2
 twice as big in y"}
 
 ```python
-image_layer_3.scale = (0.35, 0.4, 0.2047619)
+image_layer_2.scale = (0.35, 0.4, 0.2047619)
 ```
-You should see that layer 3 appears squashed - with the same width as other 
-layers, but about twice the height. This is because we set the pixel size in y 
-(which used to be 0.2047619μm) to about twice its original value (now 
+You should see that layer 2 appears squashed - with the same width as other
+layers, but about twice the height. This is because we set the pixel size in y
+(which used to be 0.2047619μm) to about twice its original value (now
 0.4μm). Bear in mind that setting the pixel sizes inappropriately can lead 
 to stretched or squashed images like this!
 
 ### 4
 
-![](fig/yeast-exercise-4.png){alt="Yeast image shown in Napari with all layers 
+![](fig/yeast-exercise-4.png){alt="Yeast image shown in Napari with all layers
 half size in y/x"}
 
 We set the pixel size in y/x to half its original value of 0.2047619μm:
 ```python
+image_layer_0.scale = (0.35, 0.10238095, 0.10238095)
 image_layer_1.scale = (0.35, 0.10238095, 0.10238095)
 image_layer_2.scale = (0.35, 0.10238095, 0.10238095)
-image_layer_3.scale = (0.35, 0.10238095, 0.10238095)
 ```
 :::::::::::::::::::::::::::::::::
 

md5sum.txt

@@ -8,7 +8,7 @@
 "episodes/what-is-an-image.md" "77453b0c3031890f96104617bcd46a49" "site/built/what-is-an-image.md" "2025-11-04"
 "episodes/image-display.md" "0d8150fdf6516bc2abb026debedfa3dd" "site/built/image-display.md" "2025-11-04"
 "episodes/multi-dimensional-images.md" "36d8d27a775bf837aaa3cf77791779fa" "site/built/multi-dimensional-images.md" "2026-06-08"
-"episodes/filetypes-and-metadata.md" "1407632ccab788a7820067e7fd5969cf" "site/built/filetypes-and-metadata.md" "2026-06-08"
+"episodes/filetypes-and-metadata.md" "719c5682d05a8c1a15079df7fd782137" "site/built/filetypes-and-metadata.md" "2026-06-08"
 "episodes/designing-a-light-microscopy-experiment.md" "9a236fbc9a48f560a786077ea9662c9c" "site/built/designing-a-light-microscopy-experiment.md" "2025-11-04"
 "episodes/choosing-acquisition-settings.md" "1bf362eeea03fe66d4e170d9803dc649" "site/built/choosing-acquisition-settings.md" "2024-08-16"
 "episodes/quality-control-and-manual-segmentation.md" "f4f883be70cd5f8cf8f24d32815064b5" "site/built/quality-control-and-manual-segmentation.md" "2026-06-05"