diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 02c5ef4bc..3361388fb 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -49,19 +49,7 @@ You can install it from here: https://github.com/powershell/powershell#get-power
 ### 2. A **.NET Core SDK**
 
 - We aim to use the latest stable version
-- You can verify the version our project is using by looking in the [global.json](https://github.com/QutEcoacoustics/audio-analysis/tree/master/build/global.json) file
-
-Recommended choice is to run the `dotnet-install` script in the [./build/](https://github.com/QutEcoacoustics/audio-analysis/tree/master/build) folder.
-
-PowerShell:
-```powershell
-> ./build/dotnet-install.ps1
-```
-
-Bash:
-```shell
-$ ./build/dotnet-install.sh
-```
+- You can verify the version our project is using by looking in the [global.json](https://github.com/QutEcoacoustics/audio-analysis/tree/master/global.json) file
 
 Alternately, you can download a SDK from here: <https://dotnet.microsoft.com/download/dotnet-core/>. Note: you want the _Build apps - SDK_ download.
 
diff --git a/docs/basics/scripting.md b/docs/basics/scripting.md
new file mode 100644
index 000000000..2706121b3
--- /dev/null
+++ b/docs/basics/scripting.md
@@ -0,0 +1,44 @@
+# Scripting AP.exe
+
+_AnalysisPrograms.exe_ works best when processing single audio files.
+This has a few advantages:
+
+**It simplifies the code**. We don't need to know about the particular
+way you store your data, or the way you want your data processed.
+
+**It allows for greater customization**. By building a set of composable
+tools, it allows you to choose what analysis is done, and when. You want it
+all? You got it. You only want the first bit done once, and the second bit done
+100 times with parameter sweeps? Go for it.
+
+**It is easier to parallelize**. You want to use your university HPC?
+Write your own distributed analysis? Or just run it in sequence? That's all
+your choice.
+
+Despite these advantages, we recognize it is useful to have example of
+how large analyses might be completed. Thus the scripts you find in this
+folder contain various examples (in various languages) of composing
+workflows with _AnalysisPrograms.exe_.
+
+**You can find a collection of example scripts here: https://github.com/QutEcoacoustics/audio-analysis/tree/master/scripts**
+
+## PowerShell
+
+You'll see a lot of scripts in that folder that are written in PowerShell.
+If you're not familiar with it, you can consider it as the Windows equivalent
+of the Bash shell. 
+
+We like PowerShell because we think the syntax is more reasonable than Bash
+and the enhanced support for dates, times, and regular expressions are well worth the investment.
+
+As of [PowerShell 6.0](https://github.com/PowerShell/PowerShell#-powershell)
+the shell is cross platform!. If you're not
+convinced, the scripts should be easy enough to reimplement in your favourite
+language (like Bash)--and we would of course appreciate any translated
+scripts sent back to us as contributed examples.
+
+## Any other language
+
+You can use any programming language to script AP.exe.
+
+R is a popular choice. We have a short guide for [using AP.exe with R](./using_r.md)
diff --git a/docs/basics/toc.yml b/docs/basics/toc.yml
index 8946c9e75..6739f0f92 100644
--- a/docs/basics/toc.yml
+++ b/docs/basics/toc.yml
@@ -10,7 +10,9 @@
 - name: Config files
   href: config_files.md
 
-- name: Scripting with R
+- name: Scripting AP.exe
+  href: scripting.md
+- name: Scripting AP.exe with R
   href: using_r.md
 
 - name: Dates
diff --git a/scripts/README.md b/scripts/README.md
index da399d8d0..aff0a88ec 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -1,62 +1,14 @@
 # Scripts
 
-_AnalysisPrograms.exe_ works best when processing single audio files.
-This has a few advantages:
-
-**It simplifies the code**. We don't need to know about the particular 
-way you store your data, or the way you want your data processed.
-
-**It allows for greater customization**. By building a set of composable
-tools, it allows you to choose what analysis done, and when. You wan't it
-all? You got it. You only want the first bit done once, and the second done
-100 times with parameter sweeps? Go for it.
-
-**It is easier to parallelize**. You want to use your university HPC?
-Write your own distributed analysis? Or just run it in sequence? That's all
-your choice.
-
-Despite these advantages, we recognize it is useful to have example of
-how large analyses might be completed. Thus the scripts you find in this
-folder contain various examples (in various languages) of composing 
-workflows with _AnalysisPrograms.exe_.
+A folder of example scripts that use AP.exe.
 
 ## Contributions appreciated!
 
-If you right a script that gets the job done for you, we'd be happy to
-include it here as an example for others to use.
-
-## PowerShell
-
-You'll see a lot of scripts in this folder that are written in PowerShell.
-If you're not familiar with it, you can consider it as the Windows equivalent
-of the Bash shell. @atruskie like's PowerShell because in their personal
-opinion, the syntax is more reasonable than Bash, and the enhanced support
-for dates, times, and regular expressions are well worth the investment.
-
-As of [PowerShell 6.0](https://github.com/PowerShell/PowerShell#-powershell)
-the shell is cross platform and well worth investigating. If you're not
-convinced, the scripts should be easy enough to reimplement in your favourite
-language (like Bash)--and we would of course appreciate any translated
-scripts sent back to us as contributed examples.
-
-## Example headers
+If you write a script that gets the job done for you, we'd be happy to
+include it here as an example for others to use. Please:
 
-We'd like to see each example script prefaced with a documentation header.
-A suggested format:
+1. fork the repository
+2. Add your script to this folder
+3. Send us a pull-request!
 
-```
-# A simple loop to XXX for a folder of files.
-# Jolene Blogs 2017
-#
-# For each audio file found,
-# - It runs does XXX
-# - It then also does YYY
-# - And sometimes does ZZZ
-# - ...
-#
-# Assumptions:
-# - AnalysisPrograms.exe is in current directory
-# - ...
 
-... script starts here ...
-```
\ No newline at end of file
diff --git a/scripts/find_ap.ps1 b/scripts/find_ap.ps1
new file mode 100644
index 000000000..1c70345fd
--- /dev/null
+++ b/scripts/find_ap.ps1
@@ -0,0 +1,35 @@
+param()
+
+$command = Get-Command AnalysisPrograms* -ErrorAction SilentlyContinue
+
+if ($null -ne $command) {
+    return $command.Path;
+    exit 0;
+}
+
+if ($IsWindows) {
+    
+    $command = Get-Command C:\AP\AnalysisPrograms.exe -ErrorAction SilentlyContinue
+
+    if ($null -ne $command) {
+        return $command.Path;
+        exit 0;
+    }
+}
+
+if ($IsLinux) {
+    $command = Get-Command /AP/AnalysisPrograms.exe -ErrorAction SilentlyContinue
+
+    if ($null -ne $command) {
+        return $command.Path;
+        exit 0;
+    }
+}
+
+Write-Error @"
+Can't find AnalysisPrograms.exe. 
+Please install it using the instructions from: 
+https://github.com/QutEcoacoustics/audio-analysis/blob/master/docs/installing.md
+"@
+
+exit 1;
\ No newline at end of file
diff --git a/scripts/generate_zooming.ps1 b/scripts/generate_zooming.ps1
index 4c8219405..177158a21 100644
--- a/scripts/generate_zooming.ps1
+++ b/scripts/generate_zooming.ps1
@@ -13,11 +13,15 @@
 # - Users will customize the below variables before running the script
 
 $working_dir = "D:/Temp/zooming"
-$csv = "$working_dir\all_oxley_creek_recordings.csv"
+$csv = "$working_dir/all_oxley_creek_recordings.csv"
 $output = $working_dir
-# The config files we copied from the ConfigFiles directory and customised for our purposes.
-$indices_config_file = "$working_dir\Towsey.Acoustic.Zooming.yml"
-$zooming_config_file = "$working_dir\SpectrogramZoomingConfig.yml"
+
+# find the path to analysis programs
+$ap_path = (Get-Command AnalysisPrograms.exe).Path
+$default_configs = Resolve-Path "$ap_path/../ConfigFiles"
+
+$indices_config_file = "$default_configs/Towsey.Acoustic.Zooming.yml"
+$zooming_config_file = "$default_configs/SpectrogramZoomingConfig.yml"
 
 $remote_user = "ubuntnu"
 $remote_server = "server.example.com"
@@ -25,17 +29,16 @@ $remote_path = "/home/ubuntu/data/original_audio"
 
 # helper functions
 
-# find the path to analysis programs
-$ap_path = (gcm AnalysisPrograms.exe).Path
 
-# just checks whether a previous run was successful 
+
+# just checks whether a previous run was successful
 function HasAlreadyRun($results_dir) {
     $log = Join-Path $results_dir "log.txt"
     if (Test-Path $log) {
         $match = Get-Content -Tail 1 $log | Select-String "ERRORLEVEL: (\d+)"
         return $match.Matches.Groups[1].Value -eq 0
     }
-    
+
     return $false
 }
 
@@ -54,14 +57,14 @@ $recordings = Import-Csv $csv
 $results = @()
 foreach ($recording in $recordings) {
     Write-Output "Starting new recording $($recording.uuid)"
-    
+
     # create a results object to store results
-    $result =  New-Object "pscustomobject" | Select-Object Download,Indices,Images
+    $result = New-Object "pscustomobject" | Select-Object Download, Indices, Images
 
     # extract all needed meta data to create a path to the remote file
     # constructs a path that looks like: ".../data/b2/b24460cf-e25e-44c9-9034-af9b0a1ddcbe_20121019-140000Z.wav
     $uuid = $recording.uuid
-    $prefix = $uuid.Substring(0,2)
+    $prefix = $uuid.Substring(0, 2)
     $date = (Get-Date $recording.recorded_date).ToString("yyyyMMdd-HHmmssZ")
     $name = "$uuid`_$date.wav"
     $remote_path = "$remote_path/$prefix/$name"
@@ -82,7 +85,7 @@ foreach ($recording in $recordings) {
     $instance_output = $local_path + "_results"
     # generate indices
 
-    if (HasAlreadyRun $instance_output) {    
+    if (HasAlreadyRun $instance_output) {
         $result.Indices = "0*"
         Write-Output "Skipping indices generation for $uuid - already completed"
     }
@@ -97,7 +100,7 @@ foreach ($recording in $recordings) {
 
     # generate zooming tiles
     $indices_dir = Join-Path $instance_output "Towsey.Acoustic"
-    AnalysisPrograms.exe DrawZoomingSpectrograms $indices_dir $zooming_config_file $instance_output -o "sqlite3" -z "Tile" -n  | IndentOutput
+    AnalysisPrograms.exe DrawZoomingSpectrograms $indices_dir $zooming_config_file $instance_output -o "sqlite3" -z "Tile" -n | IndentOutput
     $result.Images = $LASTEXITCODE
     $results += $result
 
diff --git a/scripts/indices_and_concat.ps1 b/scripts/indices_and_concat.ps1
new file mode 100644
index 000000000..400485542
--- /dev/null
+++ b/scripts/indices_and_concat.ps1
@@ -0,0 +1,91 @@
+<#
+.SYNOPSIS
+  Generates acoustic indices for multiple audio files and concatenates the output.
+.DESCRIPTION
+  Generates acoustic indices for multiple audio files and concatenates the output.
+  Expects each directory to contain audio files for one location.
+.PARAMETER $input_directories
+    A directory of audio files to process.
+.PARAMETER $output_directory
+.INPUTS
+  Optionally: input directories
+.OUTPUTS
+  Files stored in $output_directory
+.NOTES
+  Version:        2.0
+  Author:         Anthony Truskinger
+  Creation Date:  2020-01-30
+  Purpose/Change: Updated docs links, add ap finder script
+
+.EXAMPLE
+  ./indices_and_concat.ps1 D:/Stud D://Thompson -time_zone_offset "10:00" -output_directory ./output
+#>
+
+#requires -version 6
+
+param(
+    [Parameter(
+        Position = 0,
+        Mandatory = $true,
+        ValueFromRemainingArguments = $true,
+        ValueFromPipeline = $true)]
+    [System.IO.DirectoryInfo[]]$input_directories,
+
+    [Parameter(
+        Mandatory = $true)]
+    [System.IO.DirectoryInfo]$output_directory,
+
+    [Parameter(
+        Mandatory = $true)]
+    [string]$time_zone_offset,
+
+    $name_filter = "*"
+
+)
+
+# Do not continue running the script if a problem is encountered
+$ErrorActionPreference = "Stop"
+
+
+# get the path for AP.exe. When do this to resolve some nice default config files.
+# TODO: remove this when the default config file feature is implemented in AP.exe
+$ap_path = . "$PSScriptRoot/find_ap.ps1"
+$default_configs = Resolve-Path "$ap_path/../ConfigFiles"
+
+foreach ($input_directory in $input_directories) {
+    Write-Output "Processing $input_directory"
+
+    $current_group = $input_directory.Name
+
+    $audio_files = Get-ChildItem -Recurse -File $input_directory -Include "*.wav"
+    $filtered_files = $audio_files | Where-Object { $_.Name -ilike $name_filter }
+
+    $counter = 0;
+    foreach ($file in $filtered_files) {
+        $counter++
+        Write-Output "Generating indices for $file, file $counter of $($filtered_files.Count)"
+        $name = $file.Name
+
+        # for more information on how this command works, please see:
+        # https://ap.qut.ecoacoustics.info/technical/commands/analyze_long_recording.html
+        AnalysisPrograms.exe audio2csv $file "$default_configs/Towsey.Acoustic.yml" "$output_directory/$current_group/indices/$name" --no-debug --parallel
+    }
+
+    Write-Output "Now concatenating files for $current_group"
+
+    # for more information on how this command works, please see:
+    # https://ap.qut.ecoacoustics.info/technical/commands/concatenate_index_files.html
+    AnalysisPrograms.exe ConcatenateIndexFiles `
+        --input-data-directory "$output_directory/$current_group/indices" `
+        --output-directory "$output_directory" `
+        -z $time_zone_offset `
+        --file-stem-name $current_group `
+        --directory-filter "*.*" `
+        --index-properties-config "$default_configs/IndexPropertiesConfig.yml" `
+        --false-colour-spectrogram-config "$default_configs/SpectrogramFalseColourConfig.yml" `
+        --draw-images `
+        --no-debug
+
+}
+
+Write-Output "Complete!"
\ No newline at end of file
diff --git a/scripts/indices_loop.ps1 b/scripts/indices_loop.ps1
index 13ea2c940..60196a3c0 100644
--- a/scripts/indices_loop.ps1
+++ b/scripts/indices_loop.ps1
@@ -1,38 +1,60 @@
-# A simple loop to generate indices for a folder of files.
-# Karlina Indraswari 2017
-#
-# For each audio file found,
-# - It runs audio2csv to generate indices
-#
-# Assumptions:
-# - AnalysisPrograms.exe is in current directory
-# - You're working in Windows (though only trivial changes are required to work in Unix)
-# - Users will customize the below variables before running the script
-
-
-# Select the directory containing the files
-$directory = "C:\temp\Emerald River Audio Snippets\20131227\"
-# The directory to store the results
-$base_output_directory = "C:\temp\indices_output"
+<#
+.SYNOPSIS
+  # A simple loop to generate indices for a folder of files.
+.DESCRIPTION
+  Generates acoustic indices for multiple audio files.
+  Each recording will have it's indices save in a directory named after the input audio recording.
+.PARAMETER $source_directory
+    A directory of audio files to process.
+.PARAMETER $output_directory
+.INPUTS
+  Optionally: input directories
+.OUTPUTS
+  Files stored in $output_directory
+.NOTES
+  Version:        2.0
+  Author:         Karlina Indraswari & Anthony Truskinger
+  Creation Date:  2017
+  Purpose/Change: Updated docs links, add ap finder script
+
+.EXAMPLE
+  ./indices_loop.ps1 D:/Stud -time_zone_offset "10:00" -output_directory ./output
+#>
+
+param(
+    [Parameter(
+        Position = 0,
+        Mandatory = $true)]
+    $source_directory,
+    [Parameter(
+        Position = 1,
+        Mandatory = $true)]
+    $output_directory
+)
+
+$ap = . "$PSScriptRoot/find_ap.ps1"
+$default_configs = Resolve-Path "$ap_path/../ConfigFiles"
 
 # Get a list of audio files inside the directory
 # (Get-ChildItem is just like ls, or dir)
-$files = Get-ChildItem "$directory\*" -Include "*.mp3", "*.wav"
+$files = Get-ChildItem "$source_directory\*" -Include "*.mp3", "*.wav"
 
 # iterate through each file
-foreach($file in $files) {
+foreach ($file in $files) {
     Write-Output ("Processing " + $file.FullName)
 
     # get just the name of the file
     $file_name = $file.Name
 
     # make a folder for results
-    $output_directory = "$base_output_directory\$file_name"
-    mkdir $output_directory
+    $instance_output_directory = Join-Path $output_directory $file_name
+    New-Item $instance_output_directory -ItemType Directory
 
     # prepare command
-    $command = ".\AnalysisPrograms.exe audio2csv `"$file`" `".\configFiles\Towsey.Acoustic.yml`" `"$output_directory`" -n"
-    
+    # for more information on how this command works, please see:
+    # https://ap.qut.ecoacoustics.info/technical/commands/analyze_long_recording.html
+    $command = "$ap audio2csv `"$file`" `"$default_configs\Towsey.Acoustic.yml`" `"$instance_output_directory`" -n --parallel"
+
     # finally, execute the command
     Invoke-Expression $command
 }
diff --git a/scripts/ribbon_plot.ps1 b/scripts/ribbon_plot.ps1
deleted file mode 100644
index 80d32c7c8..000000000
--- a/scripts/ribbon_plot.ps1
+++ /dev/null
@@ -1,91 +0,0 @@
-# Creates a single image that shows ribbon plots stacked vertically
-# Anthony Truskinger 2018
-#
-# [2019] Deprecated: see DrawRibbonPlot command
-#
-# For each image file with the phrase "SpectralRibbon" in it's name
-#  found in a given directory it:
-# - Groups the image based on it's type (e.g. ACI-ENT-EVN)
-# - Sorts the images by date
-# - Joins the spectral ribbons together to make a ribbon plot
-# - Generates a date strip image
-# - Then joins the date strip image to the ribbon plot
-# - And saves the resulting image to the same folder
-#
-# Assumptions:
-# - The input directories contain indices results
-# - You want a grid of 1xN images (This could be paramterized in an update to the script)
-# - The user will modify the $working_dirs variable before they run the script
-
-
-$working_dirs = @(
-    "Y:\Results\20181010-115050\ConcatResult\TimedGaps\Sturt\2015July\Mistletoe",
-    "Y:\Results\20181010-115050\ConcatResult\TimedGaps\Sturt\2016Sep\Stud\CardA"
-)
-
-$image_wildcard = "*.SpectralRibbon.png"
-
-
-foreach ($working_dir in $working_dirs) {
-    Write-Output "Generating ribbon plots for $working_dir"
-    $all_images = Get-ChildItem -Recurse $working_dir -Include $image_wildcard
-
-    # sort and bucket images
-    $image_types = @{}
-
-    foreach ($image in $all_images) {
-        if ($image.FullName -match ".*(\d{8}).*__([-\w]{11})\..*") {
-            $date = [datetime]::ParseExact($Matches[1], "yyyyMMdd", [cultureinfo]::InvariantCulture)
-            $type = $Matches[2]
-
-            $image_date = [PSCustomObject]@{
-                Date = $date
-                File = $image
-            }
-
-            if (-not $image_types[$type]) {
-                $image_types[$type] = @(, $image_date)
-            }
-            else {
-                $image_types[$type] += $image_date
-            }
-        }
-        else {
-            throw "Unexpected file name pattern encountered $image"
-        }
-    }
-
-    foreach ($image_type in $image_types.Keys) {
-
-        $sorted_images = $image_types[$image_type] | Sort-Object Date
-
-        $n = $sorted_images.Count
-        # stack ribbons
-        $command = "magick montage -background '#333' -tile '1x' -gravity West -geometry +4+4 "
-        $command += ($sorted_images | ForEach-Object {
-        
-                " '$($_.File.FullName)' "
-            }) -join ' '
-        $command += " '$working_dir/stacked_ribbon_plot_$image_type`_ribbons.png'"
-
-        Write-Output "Generating ribbon plot for $image_type..."
-        Invoke-Expression $command
-    
-        # stack labels
-        $command = "magick -background '#333' -fill '#FFF'  -gravity Center  "
-        $command += ($sorted_images | ForEach-Object {
-                $date = $_.Date.ToString("yyyy-MM-dd")
-                " -size 200x40  -gravity center label:'$date'"
-            }) -join ' '
-        $command += " -append '$working_dir/stacked_ribbon_plot_$image_type`_dates.png'"
-
-        Write-Output "Generating y-axis for $image_type..."
-        Invoke-Expression $command
-
-        # combine labels, ribbons, and then stick an axis on the bottom
-        $two_map = (Get-ChildItem ($sorted_images[0].File.Directory.FullName + "/*2Maps.png")).FullName
-        Write-Output "Joining ribbon plot, y-axis, and x-axis for $image_type..."
-        magick "$working_dir/stacked_ribbon_plot_$image_type`_dates.png" "$working_dir/stacked_ribbon_plot_$image_type`_ribbons.png" +append "xwd:-" |   magick -gravity SouthEast "xwd:-" `(  "$two_map" -crop "1440x18+0+0" -background '#333' -splice 4x0+0+0 `) -append "$working_dir/stacked_ribbon_plot_$image_type.png"
-
-    }
-}
\ No newline at end of file
diff --git a/scripts/spectrogram_loop.ps1 b/scripts/spectrogram_loop.ps1
new file mode 100644
index 000000000..ef3f0a9df
--- /dev/null
+++ b/scripts/spectrogram_loop.ps1
@@ -0,0 +1,69 @@
+# Generate standard-scale spectrograms from multiple one-minute recordings.
+<#
+.SYNOPSIS
+  Generates standard spectrograms for each minute for multiple audio files.
+.DESCRIPTION
+  For every audio file found in a directory (searches recursively) this command
+  will run AP.exe to generate a set of standard spectrograms for each minute of
+  data.
+  NOTE: all spectrograms from all recordings will be saved to the same
+  directory!
+.PARAMETER $source_directory
+    A directory of audio files to process.
+.PARAMETER $output_directory
+.INPUTS
+  Optionally: input directories
+.OUTPUTS
+  Files stored in $output_directory
+.NOTES
+  Version:        2.0
+  Author:         Anthony Truskinger & Michael Towsey
+  Creation Date:  2020-01-30
+  Purpose/Change: Updated docs links, add ap finder script
+
+.EXAMPLE
+  ./spectrogrtam_loop.ps1 D:/Stud -output_directory ./output
+#>
+
+param(
+    [Parameter(
+        Position = 0,
+        Mandatory = $true)]
+    $source_directory,
+    [Parameter(
+        Position = 1,
+        Mandatory = $true)]
+    $output_directory
+)
+
+Write-Output "Draw standard-scale spectrograms of multiple one-minute recordings"
+
+
+$ap = . "$PSScriptRoot/find_ap.ps1"
+$default_configs = Resolve-Path "$ap_path/../ConfigFiles"
+
+$workshop_config = "$default_configs/Towsey.SpectrogramGenerator.yml"
+
+Write-Output "Using config File = $workshop_config"
+Write-Output "Source Directory = $source_directory"
+Write-Output "Output Directory = $output_directory"
+
+# Get a list of audio files inside the directory
+# (Get-ChildItem is just like ls, or dir)
+$recordingFiles = Get-ChildItem "$source_directory\*" -Include "*.wav"
+
+Write-Output "Found $($recordingFiles.Count) files"
+
+
+# for each file found...
+foreach ($file in $recordingFiles) {
+    Write-Output (">>>Processing: " + $file.Name)
+
+    # Run the spectrogram generation command
+    # And also tell AP.exe to talk less (with --quiet)!
+    # for more information on how this command works, please see:
+    # https://ap.qut.ecoacoustics.info/technical/commands/analyze_long_recording.html
+    . $ap audio2sonogram $file $workshop_config $output_directory --quiet
+}
+
+Write-Output "Finished!"