From 05ba85c7b488ea1ab64ef83009d191a26e18b4b5 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Fri, 23 Aug 2024 17:28:12 +1000
Subject: [PATCH] Update readme, fixes for workflow docs

---
 README.md        | 21 ++++-----------------
 docs/workflow.md |  2 +-
 2 files changed, 5 insertions(+), 18 deletions(-)

diff --git a/README.md b/README.md
index 48beb0f5..bb13b00e 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/napari-lattice)](https://pypistats.org/packages/napari-lattice)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-lattice)](https://napari-hub.org/plugins/napari-lattice)
 
-This napari plugin allows deskewing, cropping, visualisation and designing custom analysis pipelines for lattice lightsheet data, particularly from the Zeiss Lattice Lightsheet. The plugin has also been otpimixed to run in headless mode.
+This napari plugin allows deskewing, cropping, visualisation and designing custom analysis pipelines for lattice lightsheet data, particularly from the Zeiss Lattice Lightsheet. The plugin has also been optimized to run in headless mode.
 
 
 ## **Documentation**
@@ -17,10 +17,7 @@ Check the [Wiki page](https://github.com/BioimageAnalysisCoreWEHI/napari_lattice
 
 *************
 
-
-<p align="left">
-<img src="https://raw.githubusercontent.com/BioimageAnalysisCoreWEHI/napari_lattice/master/resources/LLSZ_window.png" alt="LLSZ_overview" width="500" >
-</p>
+![](deskew.png)
 
 **Functions**
 
@@ -44,25 +41,15 @@ Apply custom image processing workflows using `napari-workflows`.
 
 Support will be added for more file formats in the future.
 
-Sample lattice lightsheet data download: https://doi.org/10.5281/zenodo.7117784
+Sample lattice lightsheet data download: <https://doi.org/10.5281/zenodo.7117784>
 
 ----------------------------------
 
 This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
 
-<!--
-Don't miss the full getting started guide to set up your new package:
-https://github.com/napari/cookiecutter-napari-plugin#getting-started
-
-and review the napari docs for plugin developers:
-https://napari.org/plugins/index.html
--->
-
-
 ## Contributing
 
-Contributions are very welcome. Tests can be run with [tox], please ensure
-the coverage at least stays the same before you submit a pull request.
+Contributions are very welcome. Please refer to the [Development](./development) docs to get started.
 
 ## License
 
diff --git a/docs/workflow.md b/docs/workflow.md
index c77823a1..058a5ee4 100644
--- a/docs/workflow.md
+++ b/docs/workflow.md
@@ -5,7 +5,7 @@ The advantage of this is that you can design a multi-step automated workflow tha
 
 ## Building a Workflow
 
-You can design your workflow via GUI using [`napari-assistant](https://github.com/haesleinhuepf/napari-assistant), or in the YAML format.
+You can design your workflow via GUI using [`napari-assistant`](https://github.com/haesleinhuepf/napari-assistant), or directly in the YAML format.
 
 When building your workflow with Napari Assistant, you are actually building a *template* that will be applied to future images.
 For this reason, you need to rename your input layer to `deskewed_image`, since this is the exact value that the `lls_core` step produces.