LF only acquisition with Mantis hardware. #192

jeskesen · 2025-07-15T16:47:31Z

Addresses: #179 (partial) & #184

This reverts commit 1748131.

…ting when copying the events

…ccess Oryx camera using mmc.getCameraDevice() instead of hard-coded string

…when enabled.

…on loop

…-rean

jeskesen · 2025-07-15T17:18:17Z

Note: The author is wrong for some of these commits because the default user for the labelfree user on Mantis is Author: ieivanov <[email protected]>. I hadn't noticed when I first started committing on that system. I subsequently fixed it for that specific working copy.

jeskesen · 2025-07-15T17:25:27Z

I am unable to reproduce the pytest failure:

=============================================================================================================== 9 passed in 1.09s ===============================================================================================================
(pymmcoreplus) PS C:\Users\labelfree\shrimPy> pytest -vvv
============================================================================================================== test session starts ==============================================================================================================
platform win32 -- Python 3.10.16, pytest-7.4.4, pluggy-1.6.0 -- C:\Users\labelfree\.conda\envs\pymmcoreplus\python.exe
cachedir: .pytest_cache
rootdir: C:\Users\labelfree\shrimPy
configfile: pyproject.toml
plugins: napari-0.5.6, napari-plugin-engine-0.2.0, npe2-0.7.7
collected 9 items

mantis/tests/test_acquisition_settings.py::test_config_settings PASSED                                                                                                                                                                     [ 11%]
mantis/tests/test_acquisition_settings.py::test_device_property_settings PASSED                                                                                                                                                            [ 22%]
mantis/tests/test_acquisition_settings.py::test_time_settings PASSED                                                                                                                                                                       [ 33%]
mantis/tests/test_acquisition_settings.py::test_position_settings PASSED                                                                                                                                                                   [ 44%]
mantis/tests/test_acquisition_settings.py::test_channel_settings PASSED                                                                                                                                                                    [ 55%]
mantis/tests/test_acquisition_settings.py::test_slice_settings PASSED                                                                                                                                                                      [ 66%]
mantis/tests/test_acquisition_settings.py::test_example_settings PASSED                                                                                                                                                                    [ 77%]
mantis/tests/test_acquisition_settings.py::test_demo_settings PASSED                                                                                                                                                                       [ 88%]
mantis/tests/test_cli.py::test_main PASSED                                                                                                                                                                                                 [100%]

=============================================================================================================== 9 passed in 0.59s ===============================================================================================================

examples/acquisition_settings/example_acquisition_settings.yaml

mantis/cli/run_acquisition.py

ieivanov · 2025-07-22T19:08:17Z

mantis/cli/run_acquisition.py

        mm_config_file=mm_config_filepath,
+        lf_config_file=lf_config_filepath,
        demo_run=demo_run,
+        enable_ls_acq=False,


Fine for now, eventually we'd like to be able to determine that from the acquisition config (settings) file

Ok. We'll put this on the to-do list for later. I have also been thinking that rather than instantiating 2 acquisitions, and disabling one, we could also just not instantiate the 2nd one... and that would mean that there would be now "disabled" state.

mantis/acquisition/acq_engine.py

ieivanov · 2025-07-23T02:18:44Z

mantis/acquisition/acq_engine.py


        # Determine label-free acq timing
-        oryx_framerate = float(self.lf_acq.mmc.getProperty('Oryx', 'Frame Rate'))
+        oryx_framerate = float(


Unfortunately, there is no standard way to get the camera framerate in MicroManager - this will work for Spinnaker cameras which have a Frame Rate property exposed through the device adapter. Other camera manufacturers may call it something different. Still. I do agree with the change you are making here as self.lf_acq.mmc.getCameraDevice() is more general than Oryx. As a step further, maybe we can make a microscope_operations.get_camera_framerate() function which will standardize retrieving the camera framerate across the few different camera manufacturers we use at the Biohub?

This is a pretty weak suggestion at this point - we have hardcoded device name at many places throughout the code, we can also clean these up in another PR, I know this is not the point of this PR

Yes, let's note that for now, and deal with that when we're using a different camera.

ieivanov · 2025-07-23T02:28:12Z

mantis/acquisition/acq_engine.py

        # ls_image_saved_fn = check_ls_acq_finished

-        # Generate LF acquisition events
+        # Generate LF MDA


Do we need to check if these are enabled?

it doesn't crash anything to generate an MDA that you're not going to run... but it is wasted computation and memory.

I think I'd like to move this functionality inside of each acquisition class eventually... so I'll handle it then.

ieivanov

I think this looks good to me. I agree that is resolves #184. Let's aim to get to a point where we can stress test the pymmcore-plus acquisition engine on the mantis microscope with minimal software polishing to confirm that pymmcore-plus can do everything we need it. This will involve running a typical mantis acquisition (two arms, multiple channels, few hours imaging multiple positions) and an acquisition where we only use the LF arm. I think the only step towards that goal is finding a good data writer, correct?

ieivanov · 2025-07-23T02:42:23Z

Let me know if you need to me merge these changes, I can overwrite the failed tests check

jeskesen and others added 25 commits May 19, 2025 11:34

initial MM generated config (for Windows)

e3a3c19

Added slightly modified copy/paste of windows config for linux

1e2b05f

Modify name of Oryx camera to "Oryx"

c007de0

WIP: allowing lightsheet to be disabled

1748131

Revert "WIP: allowing lightsheet to be disabled"

3802ef4

This reverts commit 1748131.

LF can run without LS

beca9c8

style fixes

de8fbc9

small bugfixes

f01fbd3

get correct ROI size for zarr output

ff4ab69

for zarr output, remove channel dimension if <= 1

199e39a

fix Oryx camera ID in getProperty query

32cb6b9

ran black

3995abe

added checks to verify that acq engine is enabled

027a3c0

Ivan's changes to the example file for on-device development

7251e79

Temporary edits to enable LF only

dd95bab

On device hacks for debugging. revert later

8851cff

MDA really only handles channel and slice. Remove position & time set…

566c4d9

…ting when copying the events

Allow label-free config to be set on the command line. ran black.

215479a

Calculate the slice acquisition rate for LF even if LS is disabled. A…

a1761d3

…ccess Oryx camera using mmc.getCameraDevice() instead of hard-coded string

Fix logic in code which checks for light-sheet completion and aborts …

db07eb1

…when enabled.

Uncomment out acquisition & processing that happens inside the positi…

899bd6e

…on loop

removed squid configs... they should be in the configs repo

9e531e1

Added DAQ sequencing back to acquisition. Frames are now being acquired

73a52e1

fixed callback which starts the DAQ for the sequenced acquisition

efc7391

downgraded black to 22.3.0 on mantis (pymmcoreplus conda env), and re…

34a4389

…-rean

jeskesen requested a review from ieivanov July 15, 2025 17:01

Ran flake8

2e53317

fixed abort-check logic

5f75e60

jeskesen changed the title ~~LF only acquisition with actual Mantis hardware.~~ LF only acquisition with Mantis hardware. Jul 16, 2025

ieivanov reviewed Jul 22, 2025

View reviewed changes

examples/acquisition_settings/example_acquisition_settings.yaml Show resolved Hide resolved

ieivanov reviewed Jul 22, 2025

View reviewed changes

mantis/cli/run_acquisition.py Show resolved Hide resolved

ieivanov reviewed Jul 22, 2025

View reviewed changes

ieivanov reviewed Jul 23, 2025

View reviewed changes

mantis/acquisition/acq_engine.py Outdated Show resolved Hide resolved

ieivanov reviewed Jul 23, 2025

View reviewed changes

ieivanov approved these changes Jul 23, 2025

View reviewed changes

jeskesen added 2 commits July 24, 2025 09:29

changed mm_config to ls_config

a469e93

reverting example_acquisition_settings to pre-branch state

03ea1f8

jeskesen merged commit 36930a3 into czbiohub-sf:170-migrate-to-pymmcore-plus Jul 24, 2025
1 of 2 checks passed

LF only acquisition with Mantis hardware. #192

LF only acquisition with Mantis hardware. #192

Uh oh!

Conversation

jeskesen commented Jul 15, 2025

Uh oh!

jeskesen commented Jul 15, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

jeskesen commented Jul 15, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

ieivanov left a comment

Choose a reason for hiding this comment

Uh oh!

ieivanov commented Jul 23, 2025

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

jeskesen commented Jul 15, 2025 •

edited

Loading

jeskesen commented Jul 15, 2025 •

edited

Loading