Export grid from Stage Explorer to MDA positions?

[dpshepherd]

Hi @fdrgsp -

Is there an easy way in pymmcore-gui to export the current positions underlying a polygon from the Stage Explorer widget over to a MDA as individual positions? Looking at the widget code, I think one can get all of the ROIs in a grid from the widget properties - but I had trouble figuring out how to extract all of the positions from there.

What I tried:

explorer = window.get_widget("pymmcore_gui.stage_explorer_widget")
manager = explorer.roi_manager
manager.all_rois()

Gives me the shape of the ROI, but I wasn't sure how to get the individual positions out and then add to the MDA.

Thanks!

[tlambert03]

hey @dpshepherd

in a feature-experiment branch, @fdrgsp added a cool button to do exactly this: "send to MDA"

it's not on main yet, but here's what it's doing under the hood (sorry no stable API at the moment, but here's the gist):

explorer = window.get_widget("pymmcore_gui.stage_explorer_widget")
z_pos = explorer._mmc.getZPosition()
positions = [
    roi.create_useq_position(*explorer._fov_w_h(), z_pos=z_pos)
    for roi in explorer.roi_manager.all_rois()
]

mda_widget = window.get_widget("pymmcore_gui.mda_widget")
mda_widget.stage_positions.setValue(positions)

and then it should be in the MDAWidget, where you can either acquire as usual, or export/serialize

positions there will be a list of "keystone" positions, each of which has a subsequence, like this:

[
    AbsolutePosition(
        z=0.0,
        name='ROI_fdf4',
        sequence=MDASequence(
            grid_plan=GridFromPolygon(
                fov_width=512.0,
                fov_height=512.0,
                vertices=[
                    (-1780.6356938251852, -3927.016356518544),
                    (-2214.8127305115545, -3400.859190917183),
                    (-1113.7775425310288, -1682.0513154591042),
                    (-951.7864864314652, -2997.408684676615),
                    (-951.7864864314652, -3002.3284542252804)
                ]
            )
        )
    )
]

and... if you want to get the complete list of positions in the polygon, you can iterate over that subsequence:

list(positions[0].sequence)

---

obviously, there's some private stuff in there:

• explorer._mmc.getZPosition(): just to get the current Z-position
• explorer._fov_w_h(): to get current getPixelSizeUm, getImageWidth and getImageHeight

so hopefully we'll have a public API for you soon. Is the ultimate goal just to have that button that @fdrgsp added? Or would you want a programmatic API too?

[dpshepherd]

Wait - there is a button? 😆

We can use the branch...missed that.

[dpshepherd]

so hopefully we'll have a public API for you soon. Is the ultimate goal just to have that button that @fdrgsp added? Or would you want a programmatic API too?

In the long run, it might be helpful to have API access. For right now, the button would fulfill our needs.

[fdrgsp]

Hi @dpshepherd!

This is the subclass of the StegeExplorer where I added the button and here and here is where I link the button with the MDAWidget.

Do you think it can help if I create a branch of pymmcore-gui with only this update for you?

[tlambert03]

I was gonna say @fdrgsp ... that seems like a great feature. Might as well add to main

[fdrgsp]

Hey @dpshepherd, this branch of pymmcore-gui has the button (#149).

[dpshepherd]

Thanks @fdrgsp and @tlambert03! We'll give it a try.

[dpshepherd]

I can confirm the branch works and the button sends the ROI to the MDA. This is great!

A quick test led me to two questions:

1. Have you tried running a multi-channel or z-stack using the positions in the ROI? I quickly tried it with the demo config and got some unexpected behavior.

If I just select channels and order pc, then the MDA acquires all positions for the first channel and then all positions for the second channel.

If I just select Z stack and order pz then the MDA acquires all positions for the first z positions, then all positions for the second z position, etc...

I select both Channels and Z stack and order pzc then the MDA acquires all positions for first channel, first z position, then all positions for second channel, first z position, then all positions for first channel, second z position, etc...

2. Is there a way to split the ROI into the individual positions once added? Sometimes we need to modify the z position for really large samples so that a relative z stack is correctly centered.

[dpshepherd]

Also - very happy to work on implementing the above. Just wanted to make sure we doing things in a direction that matches your thoughts.

[tlambert03]

i need to double check the useq-schema code (that ultimately controls how these things are iterated)... but I have a feeling these two things are two sides of the same coin. We export the ROIs as a "single-position with a subsequence", primarily so that multiple ROIs can be exported and it all just works. But that may be what's causing the iteration order to be silly for c/z ... and splitting the ROI into individual positions may well be the solution to both that problem and your second issue (albeit, at the expense of losing which ROI it belonged too... though that could be included in the metadata somehow too).

[fdrgsp]

Hi @dpshepherd,

1. Have you tried running a multi-channel or z-stack using the positions in the ROI? I quickly tried it with the demo config and got some unexpected behavior.

I am not sure about this behavior, I will check soon! But feel free to let us know if you find a fix for that!

2. Is there a way to split the ROI into the individual positions once added?

This is not currently possible, but perhaps we could add a context menu option to the “Send to MDA” button that either:
1. sends a single position with the grid plan as a sub-sequence, or
2. sends a list of individual positions.
What do you think?

[fdrgsp]

Sorry @tlambert03 I did not see your answer :)

[dpshepherd]

This is not currently possible, but perhaps we could add a context menu option to the “Send to MDA” button that either: 1. sends a single position with the grid plan as a sub-sequence, or 2. sends a list of individual positions. What do you think?

I'm fine with the first one, since that would retain the ROI name.

I also tried running the Channel and Z positions using the sub-sequence settings on the ROI. This actually doesn't execute either the Z plan or channel switching.

[fdrgsp]

@dpshepherd I just added a context menu to the Send to MDA button for you to try. If you select the List of Single Positions, you will get a list of single position from the grid plan so you can update the z position.

Screen.Recording.2026-03-30.at.9.02.30.PM.mov

[dpshepherd]

@fdrgsp awesome! This works for both our case of changing each position starting z and the acquisition order issue we ran into. I'll work with the group to give this a go on real hardware and report back.

thank you so much!