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 · 2024-10-17T21:24:36Z

Note the mesoscope there is called "429_mesoscope_20220321" which is a slight change of text from before "429-mesoscope-2022321"

I am not sure of the implications. Please tell me how it should be called. This is meant to be MESO.1

saskiad · 2024-11-01T04:38:59Z

examples/multiplane_ophys_session.py

@@ -18,7 +17,7 @@
    subject_id="12345",
    session_type="Mesoscope",
    iacuc_protocol="12345",
-    rig_id="MESO.1",
+    rig_id="429_mesoscope_20220321",
    mouse_platform_name="disc",
    active_mouse_platform=True,
    data_streams=[


are there no active daq devices in the data stream?

Also, the camera names listed here don't match the camera names in the rig.

Add the names of the DAQ devices used in the session specified in the rig json

examples/multiplane_ophys_session.py

examples/multiplane_ophys_rig.py

saskiad · 2024-11-01T04:44:22Z

examples/multiplane_ophys_rig.py

+    pockels_cells=[
+        PockelsCell(
+            name="Pockels Cell 1",
+            polygonal_scanner="no polygon scanner",


polygonal_scanner is an optional field - I think it's better to leave it empty rather than put in a name that says there is none.

saskiad · 2024-11-01T04:45:36Z

examples/multiplane_ophys_rig.py

+            notes=None,
+            data_interface="USB",
+            computer_name="STIM",
+            channels=[],


what is the DAQ connected to?

Go to DAQChannel object of the device module and fill in the blanks for the configuration of the DAQ

saskiad · 2024-11-01T04:45:44Z

examples/multiplane_ophys_rig.py

+            notes=None,
+            data_interface="PCIe",
+            computer_name="SYNC",
+            channels=[],


ditto above

saskiad · 2024-11-01T04:45:57Z

examples/multiplane_ophys_rig.py

+            notes=None,
+            data_interface="PCIe",
+            computer_name="STIM",
+            channels=[],


saskiad · 2024-11-01T04:49:52Z

status

@@ -0,0 +1,49 @@
+COMMAND_MODE=unix2003


what is this file? Does this need to go into aind-data-schema?

saskiad

Very close - a few things.

saskiad · 2024-11-01T04:51:57Z

Note the mesoscope there is called "429_mesoscope_20220321" which is a slight change of text from before "429-mesoscope-2022321"

I am not sure of the implications. Please tell me how it should be called. This is meant to be MESO.1

It should be dashes.

axlec · 2024-11-20T23:19:36Z

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 unsubscribe<https://github.com/notifications/unsubscribe-auth/A7SAEYY5FSN7X5NHXBAECKT2BUJAPAVCNFSM6AAAAABGX2N73SVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDINBZHA3TOMRZGU>. You are receiving this because you were mentioned.Message ID: ***@***.***>

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.

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

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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

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arielleleon added 4 commits June 10, 2024 13:45

adding laser

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updating the wrong module

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pulling from latest version and adding components:

1df2ae1

renaming for consistency

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saskiad reviewed Jun 11, 2024

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arielleleon added 2 commits July 25, 2024 10:27

update to rigid format

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adding modality

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noting absence of polygon scanner

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jeromelecoq reviewed Oct 16, 2024

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jeromelecoq added 4 commits October 16, 2024 18:31

obj pmt laser pockels for Meso.1

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Linting

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Linting

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Move packages

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jeromelecoq added 3 commits October 17, 2024 13:49

up schema version

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Fix schema rig

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Fx json examples

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jeromelecoq requested a review from saskiad October 17, 2024 21:23

saskiad reviewed Nov 1, 2024

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examples/multiplane_ophys_rig.py

notes=None,

data_interface="PCIe",

computer_name="SYNC",

channels=[],

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ditto above

saskiad reviewed Nov 1, 2024

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status

@@ -0,0 +1,49 @@

COMMAND_MODE=unix2003

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what is this file? Does this need to go into aind-data-schema?

saskiad requested changes Nov 1, 2024

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arielleleon added 12 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

Add Mesoscope rig example #901

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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

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saskiad commented Nov 1, 2024

axlec commented Nov 20, 2024 via email

jeromelecoq commented Nov 20, 2024 • edited Loading

axlec commented Nov 20, 2024 via email

jeromelecoq commented Nov 20, 2024 •

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