napari intro slides

brainglobe · Nov 29, 2023 · 5829fd5 · 5829fd5
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diff --git a/img/napari-dependencies.png b/img/napari-dependencies.png
diff --git a/img/napari-highlight-controls.png b/img/napari-highlight-controls.png
diff --git a/img/napari-highlight-viewer.png b/img/napari-highlight-viewer.png
diff --git a/img/napari-install-plugins.png b/img/napari-install-plugins.png
diff --git a/img/napari.png b/img/napari.png
diff --git 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
diff --git a/slides/napari-intro.qmd 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)
+:::