Triggerscope Documentation

docs/microscope-installation-guide.md

@@ -1,5 +1,19 @@
 # Microscope Installation Guide
-
+---
+## Table of Contents
+- [Microscope Installation Guide](#microscope-installation-guide)
+  - [Table of Contents](#table-of-contents)
+  - [Install recOrder software](#install-recorder-software)
+  - [Install and configure `Micromanager`](#install-and-configure-micromanager)
+    - [Option 1 (recommended): Voltage-mode calibration installation](#option-1-recommended-voltage-mode-calibration-installation)
+    - [Option 2 (soon deprecated): retardance mode calibration installation](#option-2-soon-deprecated-retardance-mode-calibration-installation)
+    - [Option 3 (requires a Triggerscope): Setup the LCs with the triggerscope](#option-3-requires-a-triggerscope-setup-the-lcs-with-the-triggerscope)
+    - [(Optional) Enable "Phase From BF" acquisition](#optional-enable-phase-from-bf-acquisition)
+    - [Enable port access](#enable-port-access)
+  - [Connect `recOrder` to `Micromanager`](#connect-recorder-to-micromanager)
+
+
+---
 This guide will walk through a complete recOrder installation consisting of:
 1. Installing and launching the latest stable version of `recOrder` via `pip`. 
 2. Installing a compatible version of `MicroManager` and LC device drivers.
@@ -54,6 +68,9 @@ Add 5 presets to this group named `State0`, `State1`, `State2`, `State3`, and `S
 
 ![](https://github.com/mehta-lab/recOrder/blob/main/docs/images/create_preset.png)
 
+### Option 3 (requires a Triggerscope): Setup the LCs with the triggerscope
+Alternatively, the LCs can be driven with an external DAC, like the triggerscope, for hardware sequencing. To setup the triggerscope, please follow the instructions [here](./triggerscope-set-up.md).
+
 ### (Optional) Enable "Phase From BF" acquisition
 
 If you would like to reconstruct phase from brightfield, add a `Micromanager` preset with brightfield properties (e.g. moving the polarization analyzer out the light path) and give the preset a name that contains one of the following case-insensitive keywords:

docs/triggerscope-set-up.md

@@ -0,0 +1,61 @@
+# Setting up the Triggerscope
+
+This guide will walk through setting up the triggerscope (DAC device) to externally drive the LCs for hardware sequencing.
+
+---
+## Table of Contents
+- [Setting up the Triggerscope](#setting-up-the-triggerscope)
+  - [Table of Contents](#table-of-contents)
+  - [Triggerscope](#triggerscope)
+  - [Setup the Triggerscope with micromanager](#setup-the-triggerscope-with-micromanager)
+    - [Plugin the triggerscope](#plugin-the-triggerscope)
+    - [Remove/Check the Meadowlark device is not in config file](#removecheck-the-meadolwark-device-is-not-in-config-file)
+  - [Connect the Meadowlark LC control box to the Triggerscope](#connect-the-meadowlark-lc-control-box-to-the-triggerscope)
+  - [Set the LCs to `external mode`](#set-the-lcs-to-external-mode)
+  - [Launch micromanager with the new config file](#launch-micromanager-with-the-new-config-file)
+  - [FAQ / Troubleshooting](#faq--troubleshooting)
+
+---
+## Triggerscope
+The Triggerscope is ...
+The triggerscope replaces the Meadowlark control box and allows one to drive the LCs through external analog inputs. 
+
+Check the Triggerscope Firmware
+** references to triggerscope setup
+
+## Setup the Triggerscope with micromanager
+** Confirm instructions on setup.
+
+Launch Micromanager, open `Devices > Hardware Configuration Wizard...`, and add the `Triggerscope  Hub` device to your configuration.
+
+Confirm your installation by opening Devices > Device Property Browser... and confirming that `Triggerscope DAC` properties appear.
+
+
+### Plugin the triggerscope
+- Connect the triggerscope via USB
+- Connect the external power supply to the triggerscope
+- Flip on the switch
+
+### Remove/Check the Meadowlark device is not in config file
+
+
+## Connect the Meadowlark LC control box to the Triggerscope
+Using the connectors on the LC control box, connect the LC to
+Make sure to note which LC (i.e LCA and LCB) is connected to Triggerscope DAC ##.
+
+** missing pictures for the connectors
+
+## Set the LCs to `external mode`
+
+
+## Launch micromanager with the new config file
+
+
+## FAQ / Troubleshooting
+- The LCs are not changing even if I sweep the voltages on the micromanager properties. 
+  - Make sure the LC controller box is connected to the computer via USB
+  - Open CellDrive and set the LCs in ["external mode"](#set-the-lcs-to-external-mode)
+- When I change the triggerscope voltages from the MM device property manager, MM crashes
+  - [Check](#plugin-the-triggerscope) that the Triggerscope is connected via USB and connected to its power supply through the barrel connector. 
+
+