Add Mesoscope rig example #901
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Adding mesosocpe_ophys_rig.py and mesoscope_ophys_rig.json to repository |
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Identified fields that need to be updated. Please let me know if I missed anything.
In addition to the missing items, we will also need to know from Alex (or inform on) the following items:
- Automatic uploads will be happening soon. Can we use this as the current rig for now; that said, what are the plans for logging the current rig state?
- Need to know when the face camera was added. The earlier rig json did not come with a date (afaict)
examples/mesoscope_ophys_rig.py
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| ephys_assemblies=[], | ||
| fiber_assemblies=[], | ||
| stick_microscopes=[], | ||
| laser_assemblies=[], |
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Needs Laser class
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For 2P, the laser should go in the light_sources, not in laser_assemblies. (and yes, this is confusing. These are lasers on manipulators used on the ephysdome)
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This is something that Natalia handled in the past, she was not in Engineering and thus I do not know. I believe Manni He is now responsible for this.
examples/mesoscope_ophys_rig.py
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| stick_microscopes=[], | ||
| laser_assemblies=[], | ||
| patch_cords=[], | ||
| light_sources=[], |
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Add Lamp device
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Need more information on what a lamp device is? If this is part of the imaging or laser path then it is outside of our remit. Is this for camera illumination LEDS?
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This is complete. I have added both coherent scientific laser and lumen dynamics epi led to the light sources list
examples/mesoscope_ophys_rig.py
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| laser_assemblies=[], | ||
| patch_cords=[], | ||
| light_sources=[], | ||
| detectors=[], |
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Epi camera and PMTs
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This is something that Natalia handled in the past, she was not in Engineering and thus I do not know. I believe Manni He is now responsible for this.
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I have these added
examples/mesoscope_ophys_rig.py
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| patch_cords=[], | ||
| light_sources=[], | ||
| detectors=[], | ||
| objectives=[], |
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Needs to be defined
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This is something that Natalia handled in the past, she was not in Engineering and thus I do not know. I believe Manni He is now responsible for this.
examples/mesoscope_ophys_rig.py
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| lenses=[], | ||
| digital_micromirror_devices=[], | ||
| polygonal_scanners=[], | ||
| pockels_cells=[], |
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Needs to be defined
examples/mesoscope_ophys_rig.py
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| hardware_version=None, | ||
| ), | ||
| ], | ||
| calibrations=[], |
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stimulus screen calibrations
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I need advice on how to enter this information. The screen calibration is a file with a bunch of information encoded inside of it.
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@axlec if you want to send me an example of the calibration file, I can help. I expect for gamma calibration there are some input values and some readout values, which is what I would put in here, but I'm happy to demo an example if you send me a file
| data_interface=DataInterface.PCIE, | ||
| ) | ||
| ], | ||
| objectives=[], |
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The objective is one part that I could not get from Keith. I can ask Manni but she is out of town
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@axlec I need your help with this. I have no clue where to find this
| Detector( | ||
| name="PMT", | ||
| detector_type="Photomultiplier Tube", | ||
| manufacturer=Hamamatsu(name="Hamamatsu"), |
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can we get a model number/serial number for this?
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Manni could not find one
examples/multiplane_ophys_rig.py
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| pockels_cells=[ | ||
| PockelsCell( | ||
| name="Pockels Cell 1", | ||
| polygonal_scanner="something", |
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this is fine. You can also use "no polygonal scanner" as the name to make it clear
| name="Pockels Cell 1", | ||
| polygonal_scanner="something", | ||
| on_time=12.0, | ||
| off_time=13.0, |
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I'm guessing on and off need to add to 100. But let me check on that.
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These were bogus ints :/ until it's an optional parameter
| hardware_version=None, | ||
| ), | ||
| ], | ||
| calibrations=[], |
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it would be good to have monitor and laser power calibrations in here.
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I don't know where to pull the laser calibrations from yet; I need to work with Manni on this. I will pull the calibration value from the stimulus as set in the stim.cfg
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@saskiad shouldn't laser calibrations be in the session.json? They are updated weekly unless you are talking about something else
examples/multiplane_ophys_rig.py
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| ), | ||
| Axis(name="Y", direction="defined by the right hand rule and the other two axis"), | ||
| ], | ||
| modalities=set(), |
examples/multiplane_ophys_rig.py
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| rig = Rig( | ||
| describedBy="https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py", # noqa | ||
| schema_version="0.5.3", | ||
| rig_id="MESO.2", |
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rig_id needs to conform to the standard
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Is this PR still being worked on? |
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@saskiad I have added what I believe to be all the missing parts I was able to define and track. For the parts missing, I would ask Alex and team to help fill in the gaps especially with respect to how items (e.g. calibrations) get updated and tracked. |
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