diff --git a/episodes/filetypes-and-metadata.md b/episodes/filetypes-and-metadata.md index 271cf40..da2138e 100644 --- a/episodes/filetypes-and-metadata.md +++ b/episodes/filetypes-and-metadata.md @@ -314,18 +314,18 @@ 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 @@ -340,9 +340,9 @@ 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] @@ -352,40 +352,40 @@ 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) ``` :::::::::::::::::::::::::::::::::