search

espruston / PumpControls

Interfacing pumpy with micromanager and scope
1 stars 1 forks source link

Integrate pump controller code with beanshell for acquisition #1

Open dpshepherd opened 5 years ago

dpshepherd commented 5 years ago

We need to figure out how best to integrate running the stage, camera, and laser with the pumps.

I propose the following:

  1. The user finds a region of interest using the manual stage and Z piezo.
  2. The user sets up the multi-dimensional acquisition window in MicroManager 2.0 gamma so that we can pull the desired microscope settings into the acquisition script.
  3. The user runs the acquisition script, which runs pumps and acquires a user-specified number of images/z-planes for each DNA-PAINT or dSTORM cycle.

I'll upload an example of a scripted acquisition on our structured illumination microscope later this week. Example scripts on using the MM 2.0 gamma acquisition engine are found here: https://github.com/nicost/micro-manager/tree/ViewerPlusCV/scripts

This would be a good starting point and we can then add user interface and other quality of life items.

Thoughts?

espruston commented 5 years ago

This is definitely in the vein of what I had in mind. I've been running the pumps with MicroManager 1.4 due to the pump connection issue mentioned in the wiki, I'll see if the same issue persists now that we have mostly purged the NanoJ code from our methods. If we are unable to get the pumps working with 2.0 gamma, do you foresee any issue running the scope with 1.4?

dpshepherd commented 5 years ago

I think 1.4 should be OK. It is not being actively developed, but we are not trying to use any of the new features that Nico is working on with 2.0 gamma.

The scripting language is different between the two because the acquisition engine changed in 2.0 gamma. Here are the 1.4 acquisition scripts: https://micro-manager.org/wiki/Example_Beanshell_scripts

On Wed, Jun 19, 2019 at 10:06 AM Evan notifications@github.com wrote:

This is definitely in the vein of what I had in mind. I've been running the pumps with MicroManager 1.4 due to the pump connection issue mentioned in the wiki, I'll see if the same issue persists now that we have mostly purged the NanoJ code from our methods. If we are unable to get the pumps working with 2.0 gamma, do you foresee any issue running the scope with 1.4?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/espruston/PumpControls/issues/1?email_source=notifications&email_token=AGMK4VXENAJFRJ2BQVKD42DP3JKSFA5CNFSM4HZFQXSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYCLQRI#issuecomment-503625797, or mute the thread https://github.com/notifications/unsubscribe-auth/AGMK4VRGNL6B77JKAYJOCJLP3JKSFANCNFSM4HZFQXSA .