Merge pull request #14 from fercer/dev-outline

Added outline to website

Author: fercer

_toc.yml

@@ -4,6 +4,9 @@
 format: jb-book
 root: README
 parts:
+  - caption: Outline
+    chapters:
+    - file: outline.md
   - caption: Notebooks
     chapters:
     - file: notebooks/Zarr_and_Dask_for_large-scale_imaging-Part-1.ipynb

outline.md

@@ -0,0 +1,35 @@
+# Workshop outline
+
+### Setup (10 min)
+ - Getting ready the environment to code in jupyter
+
+### Give overview of the workshop (20 min)
+- Challenges of scaling up deep learning inference
+- Parallelization approach taken in this workshop 
+
+### Break (10 min)
+
+### Introduce image analysis with Dask (50 min)
+- Overview of image analysis and Dask for lazy loading
+- Image loading (using `tifffile` and `zarr` as backends) [Guided exercise]
+- Image analysis examples [Guided exercise]
+- Image analysis exercises [Unguided exercise]
+
+### Break (10 min)
+
+### Implement an inference function (50 min)
+- Overview of the `cellpose` model for cell segmentation
+- Implement the inference function for `cellpose` [Guided exercise]
+- Test implementation [Unguided exercise]
+
+### Break (10 min)
+
+### Apply the inference to a large-scale image (50 min)
+- Overview of the parallelization approach using Dask
+- Test inference function in small-scale [Unguided exercise]
+- Scale-up to the full image [Guided exercise]
+
+### Break (10 min)
+
+### Conclusion (20 min)
+- Wrap-up and recap of the learning outcomes of the workshop