diff --git a/10-multi-dimensional-data.md b/10-multi-dimensional-data.md new file mode 100644 index 00000000..be543d4f --- /dev/null +++ b/10-multi-dimensional-data.md @@ -0,0 +1,33 @@ +--- +title: Multi-dimensional data +teaching: 60 +exercises: 60 +--- + +::::::::::::::::::::::::::::::::::::::: objectives + +- Learn about multi-dimensional image data such as 3D volumetric stacks and time-lapses. +- Visualize multi-dimensional data interactively using Napari. +- Learn to use the basic functionality of the Napari GUI including overlaying masks over images. +- Construct an analysis workflow to measure properties of 3D objects in a 3D volumetric image stack. +- Construct an analysis workflow to measure changes over time from a time-lapse movie. + +:::::::::::::::::::::::::::::::::::::::::::::::::: + +:::::::::::::::::::::::::::::::::::::::: questions + +- How can we scikit-image to perform image processing tasks on multi-dimensional image data? +- How can we visualise the results using Napari? + +:::::::::::::::::::::::::::::::::::::::::::::::::: + +:::::::::::::::::::::::::::::::::::::::: keypoints + +- We open access the Napari n-dimensional image viewer with `Napari.Viewer` objects. +- `Image` and `Label` layers can be added to a viewer with `Napari.Viewer.add_image` + and `Napari.Viewer.add_label` respectively. +- Many scikit-image functions such as `skimage.filters.gaussian`, `ski.threshold.threshold_otsu`, + `ski.measure.label` and `ski.measure.regionprops` work with 3D image data. +- Iterate through time-points to analyse time-lapse movies. + +:::::::::::::::::::::::::::::::::::::::::::::::::: diff --git a/config.yaml b/config.yaml index 837a123d..bc6efb67 100644 --- a/config.yaml +++ b/config.yaml @@ -58,7 +58,7 @@ contact: 'team@carpentries.org' # - another-learner.md # Order of episodes in your lesson -episodes: +episodes: - 01-introduction.md - 02-image-basics.md - 03-skimage-images.md @@ -68,15 +68,16 @@ episodes: - 07-thresholding.md - 08-connected-components.md - 09-challenges.md +- 10-multi-dimensional-data.md # Information for Learners -learners: +learners: # Information for Instructors -instructors: +instructors: # Learner Profiles -profiles: +profiles: # Customisation --------------------------------------------- # diff --git a/md5sum.txt b/md5sum.txt index 4cc5945f..d55c8967 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -1,7 +1,7 @@ "file" "checksum" "built" "date" "CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-12-18" "LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2023-12-18" -"config.yaml" "101b3ac4b679126bb1f437306eb1b836" "site/built/config.yaml" "2023-12-18" +"config.yaml" "78121f0e6cb02000adb1d5a5962b2c61" "site/built/config.yaml" "2024-01-03" "index.md" "6e80c662708984307918adfad711e15f" "site/built/index.md" "2023-12-18" "episodes/01-introduction.md" "9755639c515fdbf752422e2e59128f63" "site/built/01-introduction.md" "2023-12-18" "episodes/02-image-basics.md" "6e18d2c930b9dbee94c6efef3c9a5622" "site/built/02-image-basics.md" "2024-01-03" @@ -12,6 +12,7 @@ "episodes/07-thresholding.md" "bc0b3a64255ef9dd359d4cf3188aba83" "site/built/07-thresholding.md" "2023-12-18" "episodes/08-connected-components.md" "c4b727de6f6f5ea4f8ef5467759c85bd" "site/built/08-connected-components.md" "2024-01-03" "episodes/09-challenges.md" "655bdca8cab5d28dc6b2c2e9275aaecc" "site/built/09-challenges.md" "2023-12-18" +"episodes/10-multi-dimensional-data.md" "09f55c6449a5e4a41c5a6d0d9817c4a0" "site/built/10-multi-dimensional-data.md" "2024-01-03" "instructors/instructor-notes.md" "b1c166a544eb4b9b91f3ac8f2dafd549" "site/built/instructor-notes.md" "2023-12-18" "learners/discuss.md" "ad762c335f99400dc2cd1a8aad36bdbd" "site/built/discuss.md" "2023-12-18" "learners/edge-detection.md" "fdbcee7436e104e6587e1cb40cd37d18" "site/built/edge-detection.md" "2023-12-18"