Update url

docs/_config.yml

@@ -1,8 +1,15 @@
-title: Just the Docs Template
-description: A starter template for a Jeykll site using the Just the Docs theme!
+title: AIC LLSM Processing
+description: Documentation for LLSM image preprocessing code used by the Advanced Imaging Center (AIC), Janelia Research Campus.
 theme: just-the-docs
 
-url: https://just-the-docs.github.io
+url: http://llsm.aicjanelia.org/
 
 aux_links:
-  Template Repository: https://github.com/just-the-docs/just-the-docs-template
+  LLSM on GitHub: https://github.com/aicjanelia/LLSM
+
+# External navigation links
+nav_external_links:
+  - title: LLSM on GitHub
+    url: https://github.com/aicjanelia/LLSM
+    hide_icon: false # set to true to hide the external link icon - defaults to false
+    opens_in_new_tab: true # set to true to open this link in a new tab - defaults to false

docs/index.md

@@ -1,8 +1,15 @@
 ---
 title: Home
 layout: home
+nav_order: 1
 ---
 
-This will be the home page for documentation for the LLSM repository.
+The Advanced Imaging Center (AIC) uses this pipeline for pre-processing of images created on our LLSM or MOSAIC systems. The pipeline consists of multiple discrete modules that are accessed via the command line using either the `llsm-pipeline` or `mosaic-pipeline` commands. The main difference in the two pipelines is the parsing of filenames and acquisition settings metadata.
 
-The pipeline consists of three discrete modules: (1) deskewing, (2) deconvolution, and (3) maximum intensity projection. The pipeline is accessed via the command line using the `llsm-pipeline` command. Each pipeline module compiles to a separate binary that can be directly executed by calling `deskew`, `decon`, or `mip` on the command line. Use the `-h` option with any command to get a list of supported arguments.
+Each of the modules compiles to a separate binary that can also be directly executed by calling it on the command line. These modules are:
+- Cropping
+- Deskewing
+- Deconvolution
+- Maximum Intensity Projection
+
+The main pipeline command and each individual module are further described in this documentation. With any command, you can also use the `-h` option to get a list of supported arguments.

docs/pipeline/install.md

@@ -5,7 +5,7 @@ parent: Pipeline Usage
 nav_order: 1
 ---
 
-## Dependencies
+# Dependencies
 
 * boost-program-options >= 1.73.0
 * boost-filesystem >= 1.73.0
@@ -15,7 +15,7 @@ nav_order: 1
 
 The pipeline assumes that all LLSM settings files have been generated by *v4.04505.Development* of the LLSM control software. Settings files generated by different versions of the LLSM control software are not likely to be parsed correctly by our parsing routine.
 
-## Installation
+# Installation
 
 The LLSM pipeline was purpose built to run on the Janelia cluster. For example, the pipeline assumes that it can directly submit jobs to an LSF cluster. We recommend using VCPKG to install the necessary dependencies.
 

docs/pipeline/pipeline.md

@@ -4,12 +4,18 @@ layout: default
 nav_order: 2
 ---
 
-## Pipeline
+# Overview
+
+This pipeline was designed to be used with the high performance computing cluster at Janelia Research Campus.  Using the overview pipeline commands requires that jobs can be submitted to an LSF cluster, but individual modules can always be used directly on the command line.  Additionally, the commands need to be on your path to be used directly. (For new AIC members, this requires a one-time set up for your cluster account.)
+
+The main input into either `llsm-pipeline` or `mosaic-pipeline` is a configuration JSON file. This configuration file is a structured way of informing the pipeline of which modules will be used, what the relevant file paths are, and any necessary parameters.
+
+## Usage
 
 ```
 usage: llsm-pipeline [-h] [--dry-run] [--verbose] input
 
-Batch deskewing, deconvolution, and mip script for LLSM images.
+Batch processing script for LLSM images.
 
 positional arguments:
   input          path to configuration JSON file