Micro-manager 2.0 with LDI laser box

I found out recently that LDI had worked with Micro-Manager to come up with a plugin for USB control of their multi-line laser box. It is available in the 2.0 gamma release of Micro-manager and I have been trying to get it working. For some reason, it does not show up in the online Devices on the MM web site, so I have no instructions. LDI claims that some people are using it, so I am hoping someone can tell me how to set it up. The analog power control looks straightforward, but I get an error when I try to adjust laser power. The shutter has multiple options and I cannot get a setup that works. Any help appreciated. Thanks- Dave

Hi @daknecht,

What is the name of the Device Adapter? I do not see anything named “LDI” in the source code that we have. I also do not recall working with them (but that does not mean much;). With “plugin” do you mean a device adapter that shows up in the hardware configuration wizard, or a plugin as something with a user interface (started from the Micro-Manager plugin menu)?

In any case, it would be best to ask LDI to document their code on the Micro-Manager website (some vendors really like to have documentation on their own site, but we have survived quite a few vendors already;). I don’t think that there is anyone but LDI (and possibly those few other LDI-Micro-Manager users out there) who can help you.

Hi Dave,

If it’s the 89North LDI, I’m not in front of it right now, but will be able to check on a system with one on Friday. From memory, think you need to enable the laser line you want (something like “ON”/“OPEN”/“ENABLED”), set the power (only steps of 1% are supported - typing in the number instead of clicking the slider arrows may help), then set a mode setting (that I can’t remember the name of) to “RUN”.

Elliot at Cairn wrote the driver I have, and I might still be remembering things from a prototype as opposed to the final version, as I’m a bit guilty of not having updated the installation on that machine in a while… Only other thing that comes to mind for now is that I think that it’s only possible to have 4 lines active simultaneously at most.

Regards,
Sunil

Ah! The 89NorthLDI!

@daknecht : it always helps to generate a trouble report (Help > Report a problem).

Hi All,

Sunil’s right, the LDI adapter is one of mine :slight_smile:

Basic operation is as follows:

  1. Once the LDI is heated up, set the functional mode setting to “RUN” (this will give you an error if the LDI isn’t heated up yet)

  2. Set the XXX-Intensity setting (where XXX is the wavelength of the laser you’re interested in)

  3. Set the XXX-Shutter setting to “OPEN” to turn the laser on and “CLOSED” to turn it off. As Sunil mentioned, you can only have 4 lasers on at a time.

Slightly more complicated operation:

  • To contol the laser intensities using an analogue voltage, set the “Intensity Control” setting to “EXT” (default is “PC”)

  • To turn the lasers on and off with a TTL singal, set the “Shutter Control” setting to “EXT” (default is “PC”)

  • There are 4 “Auto Shutter Wavelength” properties that can be set to control which lasers automatically turn on and off in respose to micromanager’s auto shutter commands (i.e., whenever a picture is taken)

@daknecht If your LDI is more than a couple of years old it might be worth contacting 89-North for a firmware update, I discovered a bug in the firmware while I was writing the device adapters which is now fixed. I can’t remember how serious the issue was or if it caused errors.

There are a few things that can cause errors like you describe, off the top of my head:

  • Trying to change the laser intensity when “Intensity Control” is set to “EXT”

  • Trying to turn a laser on when “Shutter Control” is set to “EXT”

  • Using "Auto Shutter Wavelength"s when “Shutter Control” is set to “EXT”

  • Possibly trying to turn a laser on if “Functional Mode” is not set to “RUN” (but I’m not 100% sure about that)

@nicost probably worth me writing that up properly and sticking it on the micromanager website. Is it easiest just to send you a block of text?

Elliot

Hi @Elliot_Steele

Thanks for your explanations! The micro-manager website is (still) a wiki. You can request an account (send me an email after you do so since I do not get automatically notified), I’ll approve your account, and you can add anything you like;)

Hi Elliot- Sorry for being slow to respond, I did not get a message that anyone had responded. Not sure why.
The LDI GUI was used to set the LDI to external control. It mostly works fine in MM1.4 so that should be OK.
If I just activate the Laser Power as a Group for any of the lasers, when I try to adjust the power with the slider, I immediately get an error message without even trying to go live. So it seems I don’t have correct communication between the two. In the config manager, the LDI says OK so it seems to be communicating fine there.
89North has been minimally helpful and not at all on the 2.0 driver you wrote except to alert me it was there. Since it was not on the device list, I did not even look for it. Are there any MM nightly build issues as to ones that work and ones that don’t?
Once I get the power sorted out, I will ask about the shutter. But your instructions sound like it is not an auto-shutter. Is that right? Also, is it possible the problem is the 1% step issue Sunil mentioned or should the slider work? Thanks- Dave

Slightly different issue with the LDI- With MM 1.4, since the firmware update last week, the 470 laser will only output 9% laser power (as seen in the LDI GUI) when set to full in MM 1.4. All the other lines work fine. Does anyone know what would cause that? They had problems getting the update installed and the engineer who helped did some messing beneath the hood and I fear he did something that reduced the laser power.

Hi Elliot- Trying to implement your instructions.

  1. “Once the LDI is heated up, set the functional mode setting to “RUN” (this will give you an error if the LDI isn’t heated up yet)”
    Are you referring the LDI GUI? I was told by 89North that I did not need to run the GUI at all when using the plugin.
  2. " To contol the laser intensities using an analogue voltage, set the “Intensity Control” setting to “EXT” (default is “PC”)". Sorry for my lack of knowledge here. I have a DAQ board, and with 1.4 my understanding is that I am using analog voltage to control laser power. Is that EXT? If I use the plugin, I am presuming I am bypassing the DAQ board? So with the plugin, I would be using PC? When I switch to EXT I get the error message with the power slider, so I am presuming I want the PC mode.
    3." * To turn the lasers on and off with a TTL singal, set the “Shutter Control” setting to “EXT” (default is “PC”)". Same issue- with 1.4 and the DAQ board I use the TTL. So that would be EXT? So with the plugin I would use PC as above?
  3. " * There are 4 “Auto Shutter Wavelength” properties that can be set to control which lasers automatically turn on and off in respose to micromanager’s auto shutter commands (i.e., whenever a picture is taken)" So I am unclear what I would put into a Channel group. There are two sets of auto shutter controls. One is associated with each laser line (eg. 479 Shutter) and then there is the auto shutter wavelength 1-4 which can be set to any laser wavelength. Are those different?
    Thanks- Dave

Hi Dave,

  1. You don’t need to use the LDI GUI software at all when controlling the LDI via the micromanager device adapters (in fact I suspect trying to run both at once will cause problems as the two programs will be fighting for control of the COM port). The “Functional Mode” setting should be available in micromanager’s device property browser, along with all the other settings I mentioned.

  2. The micromanager device adapters support both controlling the laser power via micromanager properties and via an external analogue voltage (i.e., via a DAQ board). If you want to control the intensity via the DAQ board then you must have the “Intensity Control” property set to “EXT”. If you want to control the laser power via the micromanager sliders you must have it set to “PC”. The same is true for shutter control.

  3. The shutter settings associated with each laser line are manual controls of whether the lasers are on or off. The Auto Shutter Channel settings determine which laser lines respond to the micromanager auto-shutter feature. Personally I’d put “Auto Shutter Channel 1” in the channel group, unless you want to have mutliple lasers on at once. This will cause the laser specified in the channel group to be turned on and off whenever micromanager takes a picture.

As for micromanager versions, unless things have changed recently, I think both 1.4 and 2.0 use the same device adapters so these steps should work the same in both 1.4 and 2.0.

The slider issue that Sunil mentioned is a bug that I need to get around to fixing. The sliders work but clicking the buttons at either end doesn’t. The documentation I was given when writing them said that the LDIs could accept intensities to a resolution less than 1%, turns out they can’t! :slight_smile:

Elliot

Hi Elliot- Thanks for the help. I got it mostly working today, but still unclear on the shutter vs auto shutter issue. You say to put the Auto Shutter Channel 1 in the channel group. But the 4 auto shutter channels seem to be specific to the 4 lasers. When I activated all 4, each was specific to a laser line. Are you saying that if I put it in the channel group instead, I should be able to switch the setting for the different channels? And what should I do with the 4 shutter open commands associated with the 4 laser lines? Is that a System startup open for all and then the autoshutter actually controls when you go Live? Does open/closed actually send light through or just allow the auto shutter to send light, ie do both have to be open? Dave

Hi Elliot- Thanks to your help, I got everything working yesterday. It makes sense now that I understand what all the bits do. I have one problem left that I hope you or Nico can help me sort out. We have an LED for white light illumination and that is triggered by the DAQ board TTL. I sometimes want to take alternating white (phase contrast) and fluorescence images. Previously, that was done through the DAQ board. With this setup, there are two different autoshutters, one for the DAQ/LeD and one for the LDI. I can get either channel by manually choosing the autoshutter in the pulldown shutter control of MM, but I have not found a way to alternate white/fluorescence channels. I tried putting both in the Channel group and switching but that doesn’t work (unless I did something wrong). Thanks- Dave

Hi Dave, glad to hear you got it all working in the end

As for alternating phase and fluorescence, I’d probably add these settings to a group:

  • LDI-Auto Shutter Wavelength 1
  • Core-Shutter

Then you should be able to make the following presets (for example 470, 555 and phase):

Fluorescence (470):

  • LDI-Auto Shutter Wavelength 1 : 470
  • Core-Shutter : LDI

Fluorescence (555):

  • LDI-Auto Shutter Wavelength 1 : 555
  • Core-Shutter : LDI

Phase:

  • LDI-Auto Shutter Wavelength 1 : None
  • Core-Shutter : DAQ/LED

If I understand correctly, micromanager should then send the auto shutter commands to the LDI when set to one of the fluorescence modes and to the LED when in phase mode. You can then set that group as the channel group and phase contrast should just appear as another channel

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What about the Solid State Shutter Device from Utilities in the configuration setup? I think I need that for the LED shutter (through Arduino) but not sure how that relates to the LDI shutter control. Dave

Hi Dave,

Sorry I thought I’d replied to this but apparently I forgot to hit the send button

You can set up as many different shutter devices as you like and MicroManager will ignore all of them except the one specified in the “Core-Shutter” property

So you should be able to add the LDI and any devices needed for controlling the LED in the hardware config wizard. Then you can set the “Core-Shutter” property to LDI and MicroManager will use the LDI and ignore the LED. Changing “Core-Shutter” to the device used to control the LED will make MicroManager use the LED and ignore the LDI.

If you then add the “Core-Shutter” property to the property group that you’re using as the channel group and add a preset where “Core-Shutter” is set to the LED device you will be able to do your phase imaging using the preset that uses the LED shutter

For anyone coming accross this thread in future, instructions for setting up the LDI are now available on the MicroManager website: 89NorthLDI - Micro-Manager