diff --git a/img/napari-dependencies.png b/img/napari-dependencies.png new file mode 100644 index 0000000..92ec022 Binary files /dev/null and b/img/napari-dependencies.png differ diff --git a/img/napari-highlight-controls.png b/img/napari-highlight-controls.png new file mode 100644 index 0000000..fc16c21 Binary files /dev/null and b/img/napari-highlight-controls.png differ diff --git a/img/napari-highlight-viewer.png b/img/napari-highlight-viewer.png new file mode 100644 index 0000000..ba1ff43 Binary files /dev/null and b/img/napari-highlight-viewer.png differ diff --git a/img/napari-install-plugins.png b/img/napari-install-plugins.png new file mode 100644 index 0000000..e006208 Binary files /dev/null and b/img/napari-install-plugins.png differ diff --git a/img/napari.png b/img/napari.png new file mode 100644 index 0000000..8eb2647 Binary files /dev/null and b/img/napari.png differ diff --git a/index.qmd b/index.qmd index c66306d..204c8ed 100644 --- a/index.qmd +++ b/index.qmd @@ -280,7 +280,10 @@ Light sheet fluorescence microscopy # [BrainGlobe website](https://brainglobe.info/){preview-link="true" style="text-align: center"} -# napari + +# [napari](https://napari.org/){preview-link="true" style="text-align: center"} + +{{< include slides/napari-intro.qmd >}} # napari demo diff --git a/slides/extra_slide.qmd b/slides/extra_slide.qmd deleted file mode 100644 index 1d699ad..0000000 --- a/slides/extra_slide.qmd +++ /dev/null @@ -1,3 +0,0 @@ -## A slide imported from outside the qmd - -This will become an example about how to use a common slide deck for the group. \ No newline at end of file diff --git a/slides/napari-intro.qmd b/slides/napari-intro.qmd new file mode 100644 index 0000000..2df9059 --- /dev/null +++ b/slides/napari-intro.qmd @@ -0,0 +1,94 @@ +## What does napari look like? + +![](img/napari.png){} + +## The napari tech stack + +:::: {.columns} + +::: {.column width="70%"} +Depends on many other open-source libraries + +* Python based, open-source +* Graphical user interface [uses `qtpy`](https://github.com/spyder-ide/qtpy) +* Rendering [in `vispy`](https://github.com/vispy/vispy#vispy-interactive-scientific-visualization-in-python) +* Images are `numpy`(-like) arrays +* Interactive scripting with `IPython` +::: + +::: {.column width="30%"} +![](img/napari-dependencies.png) +::: +:::: + +## Who has used napari before? + +:::: {.columns} + +::: {.column width="50%"} +* increasing in popularity +* still a bit immature +::: + +::: {.column width="50%"} +![](img/napari.png){width="100%"} +::: +:::: + +## Basic functionality + +On it's own, napari can: + +:::: {.columns} + +::: {.column width="40%"} +::: {.fragment .fade-in-then-semi-out fragment-index=1} +* open and display multi-dimensional images and overlays +::: +::: {.fragment .fade-in-then-semi-out fragment-index=2} +* manipulate these +::: +::: {.fragment .fade-in-then-semi-out fragment-index=3} +* install plugins +::: +::: + +::: {.column width="60%"} +::: {.r-stack} +![](img/napari-highlight-viewer.png){.fragment .fade-in-then-out fragment-index=1} + +![](img/napari-highlight-controls.png){.fragment .fade-in-then-out fragment-index=2} + +![](img/napari-install-plugins.png){.fragment .fade-in-then-out fragment-index=3} +::: +::: + +:::: + + +## Why is it good? + +It leverages Python well: + +* Open source +* Easy access to (scientific) Python (in several ways) +* Plugin installation (and development) easy +* (Relatively) good documentation +* Friendly and diverse community (including designers) +* Funding for plugins in research available + +## Why is it not-so-good? + +The immature ecosystem means: + +* things occasionally break (but lots of enthusiastic support available) +* several plugins to do the same thing (please don't reinvent the wheel - re-use other people's wheels!) +* installation trickier than e.g. Fiji/ImageJ + +## The possibilities are endless + +{{< video https://private-user-images.githubusercontent.com/21022743/233817006-67ab4165-0b9a-46aa-9731-5964448252de.mp4?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.BGo-KlId2kVmwGO8ZyrhQBVUtqvtxN8AR2kDXlILeEc >}} + +::: footer +[Napari-napari](https://github.com/jookuma/napari-napari) +::: \ No newline at end of file