From 9993b28121fa60eb6156753b4bb4c9deb9ea1926 Mon Sep 17 00:00:00 2001 From: Eduardo Hirata-Miyasaki Date: Fri, 12 May 2023 09:31:29 -0700 Subject: [PATCH 1/3] initial commit and draft --- docs/microscope-installation-guide.md | 19 ++++++++- docs/triggerscope-set-up.md | 61 +++++++++++++++++++++++++++ 2 files changed, 79 insertions(+), 1 deletion(-) create mode 100644 docs/triggerscope-set-up.md diff --git a/docs/microscope-installation-guide.md b/docs/microscope-installation-guide.md index d54a00de..93ce1109 100644 --- a/docs/microscope-installation-guide.md +++ b/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 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: diff --git a/docs/triggerscope-set-up.md b/docs/triggerscope-set-up.md new file mode 100644 index 00000000..3faa167b --- /dev/null +++ b/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 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. + + +### 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. + + From b8163984d9bc917b3e73cedee74c87075731d0f4 Mon Sep 17 00:00:00 2001 From: Talon Chandler Date: Sat, 13 May 2023 17:39:58 +0000 Subject: [PATCH 2/3] fix typos during read through --- docs/microscope-installation-guide.md | 2 +- docs/triggerscope-set-up.md | 18 +++++++++--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/microscope-installation-guide.md b/docs/microscope-installation-guide.md index 93ce1109..3efd50a0 100644 --- a/docs/microscope-installation-guide.md +++ b/docs/microscope-installation-guide.md @@ -69,7 +69,7 @@ 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) +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 diff --git a/docs/triggerscope-set-up.md b/docs/triggerscope-set-up.md index 3faa167b..d9cf0ba2 100644 --- a/docs/triggerscope-set-up.md +++ b/docs/triggerscope-set-up.md @@ -1,6 +1,6 @@ # Setting up the Triggerscope -This guide will walk through setting up the triggerscope (DAC device) to externally drive the LC's for hardware sequencing. +This guide will walk through setting up the triggerscope (DAC device) to externally drive the LCs for hardware sequencing. --- ## Table of Contents @@ -9,19 +9,19 @@ This guide will walk through setting up the triggerscope (DAC device) to externa - [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) + - [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 LC's to `external mode`](#set-the-lcs-to-external-mode) + - [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 LC's through external analog inputs. +The triggerscope replaces the Meadowlark control box and allows one to drive the LCs through external analog inputs. Check the Triggerscope Firmware -** references to triggescope setup +** references to triggerscope setup ## Setup the Triggerscope with micromanager ** Confirm instructions on setup. @@ -36,7 +36,7 @@ Confirm your installation by opening Devices > Device Property Browser... and co - Connect the external power supply to the triggerscope - Flip on the switch -### Remove/Check the Meadolwark device is not in config file +### Remove/Check the Meadowlark device is not in config file ## Connect the Meadowlark LC control box to the Triggerscope @@ -45,17 +45,17 @@ 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` +## Set the LCs 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. +- 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 it's power supply through the barrel connector. + - [Check](#plugin-the-triggerscope) that the Triggerscope is connected via USB and connected to its power supply through the barrel connector. From e148f216dadbe3a4b9ea77fd5175231df9b7a5f7 Mon Sep 17 00:00:00 2001 From: Eduardo Hirata Date: Thu, 25 May 2023 16:01:32 -0700 Subject: [PATCH 3/3] adding triggerscope description. --- docs/triggerscope-set-up.md | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/docs/triggerscope-set-up.md b/docs/triggerscope-set-up.md index d9cf0ba2..631558e9 100644 --- a/docs/triggerscope-set-up.md +++ b/docs/triggerscope-set-up.md @@ -17,20 +17,22 @@ This guide will walk through setting up the triggerscope (DAC device) to externa --- ## Triggerscope -The Triggerscope is ... -The triggerscope replaces the Meadowlark control box and allows one to drive the LCs through external analog inputs. +The Triggerscope is a device for hardware control and synchronization of cameras, lasers, shutters, galvos, stages and other optoelectronic equipment used popularily used home-built microscopes. -Check the Triggerscope Firmware -** references to triggerscope setup +** triggerscope image -## Setup the Triggerscope with micromanager -** Confirm instructions on setup. +In this case, the triggerscope is used to send 0-5V signal to the Meadowlark DS5020 controlbox to drive the LCs through external analog inputs. +*Note: the Meadowlark DS5020 is required as it converts the signals -Launch Micromanager, open `Devices > Hardware Configuration Wizard...`, and add the `Triggerscope Hub` device to your configuration. +** Check the Triggerscope Firmware -Confirm your installation by opening Devices > Device Property Browser... and confirming that `Triggerscope DAC` properties appear. +Additionally, the triggerscope can be used as a device that can be sequenced to trigger fast and precisely the optoelectronic hardware in the microscope. In Micromanager, sequencing referes to the pre-computed train of events that will trigger the different pieces of hardware fast and precisly. To create fast and precise triggering sequences, Micromanager needs to know what devices will be `sequenced` and in what order, typically predetermined by the MDA. The devices that can be sequenced include lightsources, laser combiners, stages, and DACs. Refer to the individual device adapater to check if this devices supports `hardware sequencing`. +## Setup the Triggerscope with Micromanager +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 @@ -57,5 +59,5 @@ Make sure to note which LC (i.e LCA and LCB) is connected to Triggerscope DAC ## - 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. - +- What is sequencing?