From a1158961fa15064360f66c23352d4c5fdee5eb9a Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 9 Jun 2026 09:42:36 +0100 Subject: [PATCH 1/3] fix typos found with codespell --- .github/workflows/README.md | 6 +++--- episodes/choosing-acquisition-settings.md | 4 ++-- episodes/designing-a-light-microscopy-experiment.md | 2 +- episodes/filetypes-and-metadata.md | 2 +- episodes/imaging-software.md | 4 ++-- episodes/instance-segmentation-and-measurements.md | 10 +++++----- episodes/multi-dimensional-images.md | 4 ++-- episodes/quality-control-and-manual-segmentation.md | 4 ++-- 8 files changed, 18 insertions(+), 18 deletions(-) diff --git a/.github/workflows/README.md b/.github/workflows/README.md index 59a48610..1ade97ca 100644 --- a/.github/workflows/README.md +++ b/.github/workflows/README.md @@ -39,7 +39,7 @@ $ git push origin main > - Cancel any "01 Maintain: Build and Deploy Site" workflow currently running > - Run the "02 Maintain: Check for Updated Packages" workflow and merge any PR opened to update the renv lockfile > - This should automatically run the "03 Maintain: Apply Package Cache" workflow to install packages and build the cache -> - A successful cache buid should then trigger the "01 Maintain: Build and Deploy Site" workflow +> - A successful cache build should then trigger the "01 Maintain: Build and Deploy Site" workflow ### Updating using GitHub @@ -194,7 +194,7 @@ There are no repository variables for this workflow. ## Pull Request and Review Management -Because our lessons execute code, pull requests are a security risk for any lesson and thus have security measures associted with them. +Because our lessons execute code, pull requests are a security risk for any lesson and thus have security measures associated with them. **Do not merge any pull requests that do not pass checks and do not have bots commented on them.** This series of workflows all go together and are described in the following diagram and the below sections: @@ -256,5 +256,5 @@ This emits an artifact that is the pull request number for the next action. ### Remove Pull Request Branch (pr-post-remove-branch.yaml) -Tiggered by `pr-close-signal.yaml`. +Triggered by `pr-close-signal.yaml`. This removes the temporary branch associated with the pull request (if it was created). diff --git a/episodes/choosing-acquisition-settings.md b/episodes/choosing-acquisition-settings.md index 4ed7de8c..dcc2d8d4 100644 --- a/episodes/choosing-acquisition-settings.md +++ b/episodes/choosing-acquisition-settings.md @@ -304,7 +304,7 @@ settings, with figure 5 as a great example of the different trade-offs. ::::::::::::::::::::::::::::::::::::: challenge -## Choosing acquisiton settings +## Choosing acquisition settings In the previous episode, we used an example of investigating the effects of a specific chemical on cells grown in culture. Continuing with this, which @@ -541,7 +541,7 @@ capture the two cells, no matter their alignment with the grid: micrometre wide) overlaid by a 5 micrometre pixel grid. Right - the equivalent image with a grayscale colormap" width="80%"} -Failing to meet the Nyquist critera can also result in various image artifacts +Failing to meet the Nyquist criteria can also result in various image artifacts known as 'aliasing'. For example, consider the digram below - here we have 6 small cells (blue) that are evenly spaced in the x direction. Using a pixel spacing of 10 micrometre, this produces an odd effect in our final image, where diff --git a/episodes/designing-a-light-microscopy-experiment.md b/episodes/designing-a-light-microscopy-experiment.md index d052addc..0821c0bb 100644 --- a/episodes/designing-a-light-microscopy-experiment.md +++ b/episodes/designing-a-light-microscopy-experiment.md @@ -421,7 +421,7 @@ choosing image processing and statistical analysis methods. | :----- | :------- | :------- | Brightfield | Illuminates the sample with light from one side, and images on the other | Hard to see many biological structures - usually requires contrast agents/staining to increase contrast | Phase contrast / DIC | Makes use of slight changes in the ‘phase’ of light as it passes through a sample to increase contrast | Allows unstained samples to be seen more easily -| Widefield flourescence | Fluorescent labels (with specific excitation and emission wavelengths) bind to specific biological structures | Widefield illuminates the whole sample at once, which can lead to blurry images in thicker samples +| Widefield fluorescence | Fluorescent labels (with specific excitation and emission wavelengths) bind to specific biological structures | Widefield illuminates the whole sample at once, which can lead to blurry images in thicker samples | Laser scanning confocal | A laser is scanned across the sample point by point in a raster pattern | Allows 'optical sectioning', giving clearer images in full 3D. More complex to use than widefield, also slower to acquire images. | Spinning disc confocal | An array of pinholes on a disc split the laser into hundreds of beams that move across the sample | Faster than standard laser scanning confocal | Super-resolution | Wide range of methods that break the classic 'diffraction limit' of light, allowing resolutions down to tens of nanometres | More complex to use than standard widefield / confocal diff --git a/episodes/filetypes-and-metadata.md b/episodes/filetypes-and-metadata.md index b141bb18..ca311691 100644 --- a/episodes/filetypes-and-metadata.md +++ b/episodes/filetypes-and-metadata.md @@ -237,7 +237,7 @@ During the [setup instructions](../learners/setup.md), we installed the If you want to open more types of file, you will have to install the relevant reader following the -[intructions in the BioIO docs](https://bioio-devs.github.io/bioio/OVERVIEW.html). +[instructions in the BioIO docs](https://bioio-devs.github.io/bioio/OVERVIEW.html). Note the `bioio-bioformats` reader should allow a wide range of file formats to be read. diff --git a/episodes/imaging-software.md b/episodes/imaging-software.md index febfb56a..7ae8ceee 100644 --- a/episodes/imaging-software.md +++ b/episodes/imaging-software.md @@ -86,7 +86,7 @@ Plugins, in contrast to scripts, are focused on adding optional new features to a piece of software (rather than automating use of existing features). They allow members of the community, outside the main team that develops the software, to add features they need for a particular image type or processing -task. They're designed to be re-useable so other members of the community can +task. They're designed to be reusable so other members of the community can easily benefit from these new features. :::::::::::::::::::::::::::::::::::::::::::::::: @@ -254,7 +254,7 @@ menu-bar of Napari and select: You should see a fluorescence microscopy image of some cells: -![](fig/cells-napari.png){alt="A screenshot of a flourescence microscopy image +![](fig/cells-napari.png){alt="A screenshot of a fluorescence microscopy image of some cells in Napari"} ## Napari's User interface diff --git a/episodes/instance-segmentation-and-measurements.md b/episodes/instance-segmentation-and-measurements.md index 8c06cf08..5fc4fcb8 100644 --- a/episodes/instance-segmentation-and-measurements.md +++ b/episodes/instance-segmentation-and-measurements.md @@ -8,7 +8,7 @@ exercises: 15 - How do we perform instance segmentation in Napari? - How do we measure cell size with Napari? -- How do we save our work to create re-usable workflows? +- How do we save our work to create reusable workflows? :::::::::::::::::::::::::::::::::::::::::::::::: @@ -20,7 +20,7 @@ exercises: 15 - Calculate the number of cells and average cell volume. -- Save and edit your workflow to re-use on subsequent images. +- Save and edit your workflow to reuse on subsequent images. - Perform more complex cell shape analysis using scikit-image's `regionprops`. @@ -365,7 +365,7 @@ again. viewer.layers.remove('instance_seg') eroded_semantic_seg = viewer.layers['eroded ball 10'].data -# Create a new instace segmentation using the eroded mask +# Create a new instance segmentation using the eroded mask instance_seg = label(eroded_semantic_seg) viewer.add_labels(instance_seg) @@ -498,7 +498,7 @@ There are 11 individual nuclei You now have a correct instance segmentation. You could return to using the napari-skimage plugin to calculate the sizes -of each nucleus and export the results to a speadsheet or your preferred +of each nucleus and export the results to a spreadsheet or your preferred analysis software using the `Save Results` function. However you've probably picked up enough Python during this course to complete the analysis you need with just the Napari console. Let's give it a try. The following commands @@ -608,7 +608,7 @@ These numbers provide a good quantitative measure of the quantity and volume of cell nuclei suitable for an experiment investigating how these quantities change over time. -We can save our work from the console for re-use on data from subsequent +We can save our work from the console for reuse on data from subsequent time points, creating a repeatable measurement workflow. ```python diff --git a/episodes/multi-dimensional-images.md b/episodes/multi-dimensional-images.md index f94964a4..a454fc62 100644 --- a/episodes/multi-dimensional-images.md +++ b/episodes/multi-dimensional-images.md @@ -156,7 +156,7 @@ Next, let's look at a 3D image where an additional (fourth) dimension contains data from different 'channels'. Remove the brain image and select: `File > Open Sample > napari builtins > Cells (3D+2Ch)` -![](fig/cells-napari.png){alt="A screenshot of a flourescence microscopy image +![](fig/cells-napari.png){alt="A screenshot of a fluorescence microscopy image of some cells in Napari"} Image channels can be used to store data from multiple sources for the same @@ -178,7 +178,7 @@ This diagram shows an example of a 2D image with channels, but this can also be extended to 3D images, as we will see now. Fluorescence microscopy images, like the one we currently have open in Napari, -are common examples of images with multiple channels. In flourescence +are common examples of images with multiple channels. In fluorescence microscopy, different 'flourophores' are used that target specific features (like the nucleus or cell membrane) and emit light of different wavelengths. Images are taken filtering for each of these wavelengths in turn, giving one diff --git a/episodes/quality-control-and-manual-segmentation.md b/episodes/quality-control-and-manual-segmentation.md index 613bf273..3972f7a7 100644 --- a/episodes/quality-control-and-manual-segmentation.md +++ b/episodes/quality-control-and-manual-segmentation.md @@ -29,7 +29,7 @@ number of cells in an image. First, let's open one of Napari's sample images with: `File > Open Sample > napari builtins > Cells (3D + 2Ch)` -![](fig/cells-napari.png){alt="A screenshot of a flourescence microscopy image +![](fig/cells-napari.png){alt="A screenshot of a fluorescence microscopy image of some cells in Napari"} ## Quality control @@ -623,7 +623,7 @@ These models learn to segment images based on provided 'groundtruth' data. This interest. While generating this manual groundtruth is still slow and time consuming, the advantage is that we only need to segment a small subset of our images (rather than the entire thing). Also, once the model is trained, it can -be re-used on similar image data. +be reused on similar image data. It's worth bearing in mind that automated methods are rarely perfect (whether they're classic image processing, machine learning or deep learning based). It's From dbd58a88b8c77bd202da5675f52271369b858021 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 9 Jun 2026 11:32:22 +0100 Subject: [PATCH 2/3] undo typo fix in auto-generated workflow file --- .github/workflows/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/README.md b/.github/workflows/README.md index 1ade97ca..c3f5f69c 100644 --- a/.github/workflows/README.md +++ b/.github/workflows/README.md @@ -39,7 +39,7 @@ $ git push origin main > - Cancel any "01 Maintain: Build and Deploy Site" workflow currently running > - Run the "02 Maintain: Check for Updated Packages" workflow and merge any PR opened to update the renv lockfile > - This should automatically run the "03 Maintain: Apply Package Cache" workflow to install packages and build the cache -> - A successful cache build should then trigger the "01 Maintain: Build and Deploy Site" workflow +> - A successful cache buid should then trigger the "01 Maintain: Build and Deploy Site" workflow ### Updating using GitHub From bfc81d9278fd098538168e5a3b7cc4fed8d6bfa8 Mon Sep 17 00:00:00 2001 From: Stella <30465823+stellaprins@users.noreply.github.com> Date: Tue, 9 Jun 2026 11:38:36 +0100 Subject: [PATCH 3/3] undo other typos in auto-generated readme --- .github/workflows/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/README.md b/.github/workflows/README.md index c3f5f69c..59a48610 100644 --- a/.github/workflows/README.md +++ b/.github/workflows/README.md @@ -194,7 +194,7 @@ There are no repository variables for this workflow. ## Pull Request and Review Management -Because our lessons execute code, pull requests are a security risk for any lesson and thus have security measures associated with them. +Because our lessons execute code, pull requests are a security risk for any lesson and thus have security measures associted with them. **Do not merge any pull requests that do not pass checks and do not have bots commented on them.** This series of workflows all go together and are described in the following diagram and the below sections: @@ -256,5 +256,5 @@ This emits an artifact that is the pull request number for the next action. ### Remove Pull Request Branch (pr-post-remove-branch.yaml) -Triggered by `pr-close-signal.yaml`. +Tiggered by `pr-close-signal.yaml`. This removes the temporary branch associated with the pull request (if it was created).