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Triggerscope Documentation #372

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initial commit and draft
edyoshikun committed May 12, 2023
commit 9993b28121fa60eb6156753b4bb4c9deb9ea1926
19 changes: 18 additions & 1 deletion docs/microscope-installation-guide.md
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@@ -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 LC's 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:
61 changes: 61 additions & 0 deletions docs/triggerscope-set-up.md
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# Setting up the Triggerscope

This guide will walk through setting up the triggerscope (DAC device) to externally drive the LC's 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 Meadolwark 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 LC's 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 LC's through external analog inputs.

Check the Triggerscope Firmware
** references to triggescope 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.

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I'd benefit from details about what the "Sequencing" settings do.


### Plugin the triggerscope
- Connect the triggerscope via USB
- Connect the external power supply to the triggerscope
- Flip on the switch

### Remove/Check the Meadolwark 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 LC's to `external mode`


## Launch micromanager with the new config file


## FAQ / Troubleshooting
- The LC's 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 it's power supply through the barrel connector.