Add Mesoscope rig example #901

arielleleon · 2024-04-24T23:36:43Z

No description provided.

arielleleon · 2024-04-24T23:37:19Z

Adding mesosocpe_ophys_rig.py and mesoscope_ophys_rig.json to repository

arielleleon

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)

arielleleon · 2024-04-25T16:48:34Z

examples/mesoscope_ophys_rig.py

+    ephys_assemblies=[],
+    fiber_assemblies=[],
+    stick_microscopes=[],
+    laser_assemblies=[],


Needs Laser class

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)

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

arielleleon · 2024-04-25T16:53:42Z

examples/mesoscope_ophys_rig.py

+    laser_assemblies=[],
+    patch_cords=[],
+    light_sources=[],
+    detectors=[],


Epi camera and PMTs

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.

I have these added

arielleleon · 2024-04-25T16:54:01Z

examples/mesoscope_ophys_rig.py

+    patch_cords=[],
+    light_sources=[],
+    detectors=[],
+    objectives=[],


Needs to be defined

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.

arielleleon · 2024-04-25T16:54:12Z

examples/mesoscope_ophys_rig.py

+    lenses=[],
+    digital_micromirror_devices=[],
+    polygonal_scanners=[],
+    pockels_cells=[],


Needs to be defined

Same as the others.

arielleleon · 2024-04-25T16:55:48Z

examples/mesoscope_ophys_rig.py

+            hardware_version=None,
+        ),
+    ],
+    calibrations=[],


stimulus screen calibrations

I need advice on how to enter this information. The screen calibration is a file with a bunch of information encoded inside of it.

@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

Gamma calibration would be valuable. was this resolved?

saskiad · 2024-06-11T23:17:22Z

examples/multiplane_ophys_rig.py

+            data_interface=DataInterface.PCIE,
+        )
+    ],
+    objectives=[],


still missing objective!

The objective is one part that I could not get from Keith. I can ask Manni but she is out of town

@axlec I need your help with this. I have no clue where to find this

We can check the order. Those are custom from an optic company in Florida. I know at some point, there was some effort to switch to a thorlabs slimmer design.

saskiad · 2024-06-11T23:17:38Z

examples/multiplane_ophys_rig.py

+        Detector(
+            name="PMT",
+            detector_type="Photomultiplier Tube",
+            manufacturer=Hamamatsu(name="Hamamatsu"),


can we get a model number/serial number for this?

Manni could not find one

I can get this. Those are standard and I think I have the record of it. It is possible Natalia changed them. Usually there is a sticker on the back end face of the PMT.

examples/multiplane_ophys_rig.py

saskiad · 2024-06-11T23:18:36Z

examples/multiplane_ophys_rig.py

+            name="Pockels Cell 1",
+            polygonal_scanner="something",
+            on_time=12.0,
+            off_time=13.0,


I'm guessing on and off need to add to 100. But let me check on that.

These were bogus ints :/ until it's an optional parameter

This has been added in the latest version of aind-data-schema

examples/multiplane_ophys_rig.py

saskiad · 2024-06-11T23:21:02Z

examples/multiplane_ophys_rig.py

+        ),
+        Axis(name="Y", direction="defined by the right hand rule and the other two axis"),
+    ],
+    modalities=set(),


missing modalities!

examples/multiplane_ophys_rig.py

mekhlakapoor · 2024-06-28T23:19:59Z

Is this PR still being worked on?

arielleleon · 2024-07-25T18:13:22Z

@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.

jeromelecoq · 2024-10-16T20:55:03Z

examples/multiplane_ophys_rig.py

+        Detector(
+            name="PMT",
+            detector_type="Photomultiplier Tube",
+            manufacturer=Hamamatsu(name="Hamamatsu"),


I can get this. Those are standard and I think I have the record of it. It is possible Natalia changed them. Usually there is a sticker on the back end face of the PMT.

jeromelecoq · 2024-10-16T20:56:02Z

examples/multiplane_ophys_rig.py

+            data_interface=DataInterface.PCIE,
+        )
+    ],
+    objectives=[],


We can check the order. Those are custom from an optic company in Florida. I know at some point, there was some effort to switch to a thorlabs slimmer design.

examples/multiplane_ophys_rig.py

jeromelecoq · 2024-10-16T20:58:00Z

examples/mesoscope_ophys_rig.py

+            hardware_version=None,
+        ),
+    ],
+    calibrations=[],


Gamma calibration would be valuable. was this resolved?

examples/multiplane_ophys_rig.json

jeromelecoq · 2024-11-20T23:24:01Z

its 6mm according to the thorlabs website.
________________________________ From: arielleleon @.> Sent: Wednesday, November 20, 2024 3:08 PM To: AllenNeuralDynamics/aind-data-schema @.> Cc: Alex Cahoon @.>; Mention @.> Subject: Re: [AllenNeuralDynamics/aind-data-schema] Add Mesoscope rig example (PR #901) @arielleleon commented on this pull request.
________________________________ In examples/multiplane_ophys_rig.json<#901 (comment)>:

"manufacturer": {

"name": "Thorlabs", + "abbreviation": null, + "registry": { + "name": "Research Organization Registry", + "abbreviation": "ROR" + }, + "registry_identifier": "04gsnvb07" + }, + "model": "MVL6WA", + "path_to_cad": null, + "port_index": null, + "additional_settings": {}, + "notes": null, + "focal_length": "6", + "focal_length_unit": "millimeter", Will check with Alex - this may be 6" — Reply to this email directly, view it on GitHub<#901 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7SAEYY5FSN7X5NHXBAECKT2BUJAPAVCNFSM6AAAAABGX2N73SVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDINBZHA3TOMRZGU. You are receiving this because you were mentioned.Message ID: @.***>

I think we should remove any metadata for off the shelf parts. It is endless otherwise. I would recommend just storing the part numbers and manufacturer, this is sufficient information. This is the practice in methods of papers.

axlec · 2024-11-20T23:25:36Z

Agreed, 100%

…

________________________________ From: Jerome Lecoq ***@***.***> Sent: Wednesday, November 20, 2024 3:24 PM To: AllenNeuralDynamics/aind-data-schema ***@***.***> Cc: Alex Cahoon ***@***.***>; Mention ***@***.***> Subject: Re: [AllenNeuralDynamics/aind-data-schema] Add Mesoscope rig example (PR #901) its 6mm according to the thorlabs website.

________________________________ From: arielleleon @.> Sent: Wednesday, November 20, 2024 3:08 PM To: AllenNeuralDynamics/aind-data-schema @.> Cc: Alex Cahoon @.>; Mention @.> Subject: Re: [AllenNeuralDynamics/aind-data-schema] Add Mesoscope rig example (PR #901<#901>) @arielleleon<https://github.com/arielleleon> commented on this pull request.

________________________________ In examples/multiplane_ophys_rig.json<#901 (comment)<#901 (comment)>>: * "manufacturer": { * "name": "Thorlabs", + "abbreviation": null, + "registry": { + "name": "Research Organization Registry", + "abbreviation": "ROR" + }, + "registry_identifier": "04gsnvb07" + }, + "model": "MVL6WA", + "path_to_cad": null, + "port_index": null, + "additional_settings": {}, + "notes": null, + "focal_length": "6", + "focal_length_unit": "millimeter", Will check with Alex - this may be 6" — Reply to this email directly, view it on GitHub<#901 (comment)<#901 (comment)>>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A7SAEYY5FSN7X5NHXBAECKT2BUJAPAVCNFSM6AAAAABGX2N73SVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDINBZHA3TOMRZGU. You are receiving this because you were mentioned.Message ID: @.***> I think we should remove any metadata for off the shelf parts. It is endless otherwise. I would recommend just storing the part numbers and manufacturer, this is sufficient information. — Reply to this email directly, view it on GitHub<#901 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7SAEY5MJMRDQGDFIWYQ2PD2BUK2RAVCNFSM6AAAAABGX2N73SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOBZG42DAMRRGU>. You are receiving this because you were mentioned.Message ID: ***@***.***>

…e rig.json.

- Add NI-DAQ componenets; still needs review. - Fixes room name inconsistencies.

arielleleon · 2025-01-22T01:39:53Z

Latest fixes should contain all that we spoke about. In case I didn't this somewhere else: I could not get an updated wiring diagram from SIPE. They will need to add relevant DAQ connections. The wiring diagram they passed me was out of date

saskiad · 2025-01-23T21:52:55Z

examples/multiplane_ophys_session.py

+                Modality.POPHYS,
+                Modality.BEHAVIOR_VIDEOS,
+            ],
+            daq_names=["NI PCIe-6612", "NI PCIe-6321", "NI USB-6001", "NI OEM-6001"],


These names don't match the ones in the rig file. Those were STIM DAQ, SYNC DAQ, VBEB DAQ. The names have to match between the rig and the session

saskiad

fix the daq names in the session file.
We can address the daq channels when we have a full wiring diagram.

arielleleon · 2025-01-23T22:03:07Z

@saskiad - those names should be synchronized now

testing on runner

6f4f16a

arielleleon requested a review from saskiad April 24, 2024 23:36

arielleleon linked an issue Apr 24, 2024 that may be closed by this pull request

Add Mesoscope rig example #890

Open

arielleleon added 3 commits April 24, 2024 16:41

ran linters

3d67a51

noqa

693757d

adding docstring:

fa70516

arielleleon changed the title ~~testing on runner~~ Add Mesoscope rig example Apr 25, 2024

arielleleon commented Apr 25, 2024

View reviewed changes

arielleleon added 4 commits June 10, 2024 13:45

adding laser

12ec3d3

updating the wrong module

d630730

pulling from latest version and adding components:

1df2ae1

renaming for consistency

1bc0679

saskiad reviewed Jun 11, 2024

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saskiad reviewed Jun 11, 2024

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examples/multiplane_ophys_rig.py Show resolved Hide resolved

saskiad reviewed Jun 11, 2024

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arielleleon added 2 commits July 25, 2024 10:27

update to rigid format

953cf27

adding modality

f0414cc

noting absence of polygon scanner

7eb6a18

jeromelecoq reviewed Oct 16, 2024

View reviewed changes

jeromelecoq added 4 commits October 16, 2024 18:31

obj pmt laser pockels for Meso.1

1bfd91e

Linting

cf892fa

Linting

d4326ce

Move packages

9ceb6af

arielleleon added 21 commits December 4, 2024 15:59

Correct gains listed for behavior cameras.:

8363720

Correct spelling for disc.

d1371f9

Attempt to leave polygonal scanner as an empty str.

7f8e7c7

Fix mouse_platform_name in session.

c3f948f

Camera names of data streams should match the camera names in from th…

798f738

…e rig.json.

Add NIDaqs to data streams.

fba8788

Lint.

892a6d5

Lint.

5fd07f6

Sort imports.

fdb83ba

Fix rig_id name formatting.

eb6c33f

Generate multiplane rig.json

a3fdcf0

Generate session.json.

3e83d0d

Fix rig_id formatting in rig generator.

4914e1c

Resolve review issues.

4a2b84d

- Add NI-DAQ componenets; still needs review. - Fixes room name inconsistencies.

Remove channel_name from DAQDevice.

8f5d885

Generate multiplane_ophys_rig.json from python file.

26683f4

Lint.

c609581

Generate multiplane_ophys_session.json from python example.

4e28667

Remove extraneous file.

b4cdbe5

Add DAQ devices and additional devices to rig schema.

e4a1449

Generate multiplane_ophys_session.json.

da376ba

saskiad self-requested a review January 23, 2025 21:48

saskiad reviewed Jan 23, 2025

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saskiad requested changes Jan 23, 2025

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arielleleon added 2 commits January 23, 2025 13:57

Sync DAQ names between multiplane-ophys session and rig jsons.

5b089a6

Generate session.json example from updated python script.

28fd456

Add Mesoscope rig example #901

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arielleleon commented Apr 24, 2024

arielleleon commented Apr 24, 2024

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mekhlakapoor commented Jun 28, 2024

arielleleon commented Jul 25, 2024

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jeromelecoq commented Nov 20, 2024 • edited Loading

axlec commented Nov 20, 2024 via email

arielleleon commented Jan 22, 2025

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arielleleon commented Jan 23, 2025

jeromelecoq commented Nov 20, 2024 •

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