Submitting procedures

[vncntprvst]

Hello,
At the moment, it is only possible to submit resources and taxonomies . However, many procedures are not available (e.g., headpost implantation). I don't see a way to create a custom user-defined procedure either. This is an issue because it means BrainSTEM cannot fully replace other record keeping systems used in the lab.
Would it make sense to allow users to submit procedures ?
Thanks,
Vincent

[petersenpeter]

Hi Vincent.

Thanks for your suggestion! We are presently not allowing the end user to add procedures, but we wish to grow the available procedures through input from the community. I would be happy to work with you on adding this procedure. What parameters would you like to have to describe a headpost implantation? And what other procedures are you missing?

/ Peter

[vncntprvst]

Hi Peter.

For a headpost procedure, the most important field is the date :)
You don't want to use a prep with an old implant (~2 / 3 months, YMMV).
Other fields could be:

• Type of headpost
• Ground pin ? Y/N, type, location
• Marker / reference points (e.g., for future cranios)? Y/N, coordinates.

Non-exhaustive list of surgery / implant procedures that could be added:

• EEG / LFP
• EMG
• Transparent Headcap (for wide-field imaging)
• GRIN lens
• Transmitter for telemetry
• Catheter and Vascular Access Button
• Drug delivery cannula

Happy to help document these!

[vncntprvst]

Hi Peter.
Just a note on the topic of headpost procedures: I realized there is one in the AIND data schema.
See Headframe in the procedures_schema.
Example usage: https://github.com/AllenNeuralDynamics/aind-data-schema/blob/8f86f18ac3baeee011f470a7323cdb62692f6aab/examples/ophys_procedures.py#L41.

[petersenpeter]

Hi Vincent,

Thank you for the link. All procedures share a set of fields, including the date and time of the procedure. You can view the shared fields here. Regarding additional fields, my suggestion would be something like:

• Material (e.g., titanium, aluminum, plastic)
• Shape or Type (circular, oval, hexagonal)
• Skull preparation (cleaning steps)
• Attachment method (e.g., dental cement, super glue, epoxy)

Please let me know what you think. You mentioned a ground pin; is this related to the headpost? Could you elaborate on the markers?
EEG/LFP and EMG are more related to data acquisition. I am also curious to hear your suggestions for implementing the other proposed procedures: GRIN lens, catheter, and cannula.

[petersenpeter]

Hi Vincent. Let me know your thoughts on the suggested fields.

[vncntprvst]

Hi Peter,
very sorry for the delay. I'll reply to you tomorrow.
Vincent

[vncntprvst]

Hi Peter,
The additional fields for the headpost implantation look good to me.
If the Materials field includes suggestions, I would add stainless steel to the list, which is pretty common.
About the ground pin: this is a pin (sometimes soldered to a screw that is attached to the skull), that connects the probe, for ephys experiments. This is commonly implanted in the same procedure as the headpost, that why I mention it. But it could be a separate procedure, although that sounds a bit cumbersome to ask the user to add so many separate records of adjacent procedures. Alternatively, it could noted in the Skull preparation field, I guess. Same thing for the the markers. Typically, we need to mark coordinates for the craniotomy, but we do not perform the craniotomy (or craniectomy) procedure until after the subject is ready to be recorded (e.g., after training, or viral expression, etc).
I'll get back to you about the other procedures mentioned.

[petersenpeter]

Hi Vincent

I would suggest adding ground/reference screw as a separate procedure with its own coordinates and such. We do not currently have that, but I will add it as well.

[vncntprvst]

Hi Peter,
Sorry for the lack of feedback, I do not have time to work on this a the moment. Just wanted to point out that EEG, LFP and EMG implants are specific procedures, in addition to be be recording methods. The details about electrode / connector types and even more so location are essential to analyze the data.

[petersenpeter]

Thanks Vincent.

We will push a change to address your feedback. I will keep you updated.

/ Peter

[petersenpeter]

Dear Vincent,

The changes addressing some of your requests are now on our production server (BrainSTEM.org). I added a headpost implant and a headcap. I also included EEG and EMG implants, reference electrodes, and catheters.

I have not settled on a good solution for coordinates outside of our other procedures but am still working on this.

Perhaps we can continue the conversation in person in Boston.

Best,
Peter

[vncntprvst]

Awesome. Thank you! I'll take a look at this, and for sure we can continue this conversation when you're here.
@Mel-Gonzalez2k, @kaid0212, could you log in to BrainSTEM and test these new features as well before the workshop?
Thanks

[petersenpeter]

Great. And please let us know of any feedback!

[vncntprvst]

Hi Peter:
A couple of feedback comments:

• When editing a procedure, if one clicks on Save and Exit, instead of the Confirm icon, then the page kind of freezes, and the entry is lost. Cliking on Save and Exit should automatically confirm the entry, and close it.
• In the filters (e.g., for Procedures), the Users drop-down menu lists all BrainSTEM users. It would be more convenient to list by default only users from the current user's team.

[vncntprvst]

• When adding a setup, if "Head-fixed Awake" is selected in Setup category, Setup type defaults to Head-fixed disc.
  
  No other option is available (e.g., Running wheel), and also no "Other" option, which should be available when new Taxonomies have been submitted but not approved yet.

[petersenpeter]

Hi Vincent

The temporary entry is currently only available for strains. We are working on implementing it for the other models. I approved your Setup type submission so it will be available now. The head-fixed disc was the only setup type we had that belonged to the Setup category Head-Fixed Awake.

There is an Other option, but you have to select the Unknown category first.

[vncntprvst]

Ok. Thanks for the quick approval!

[petersenpeter]

Thanks Vincent.

The page freeze is, unfortunately, a bug we discovered after a recent update, but we will address it soon.

I agree about the Save and Exit logic.

I will implement a teams filter

[vncntprvst]

For Sessions: the fact that the Session name should unique across BrainSTEM is a VERY important requirement.

I would mention that requirement directly above the field, not just in the information pop-up, because many users will miss it (2 for 2 missed it in our tests :) ).

[petersenpeter]

Are you saying it is too strict, or that we need to make it more prominent to the user?

We can talk about this more on Wednesday.

[vncntprvst]

I would make it more prominent, especially if it is such a strict requirement.
There's a case to make it less strict too (e.g., enforcing at the level of a team, not community-wide).
We can talk more on Wednesday.

[julia-dziubek]

Hey Peter, great workshop, thanks! What is the best way to submit all the following:

• surgeries: prism implantation, blood pressure sensor implantation, ECG sensor implantation, breathing sensor implantation, ganglion viral injection, infraorbital nerve constriction injury surgery, injection of virus into muscles/other peripheral tissues
• experimental types: Von Frey mechanical pain test, Hargreaves thermal sensitivity test, formalin pain assay, pinprick mechanical pain test, breathing recording, ECG/BP recording, habituation to experimental setups/researcher (to handling and ip injection), subcutaneous, IV, and IP injections of various substances, thermal laser pain stimulation to the face vs hind paws
• how would you submit acquisition of the data that was collected by observation and taking notes, such as mouse's responses to von Frey pain stimulus?
• for categorical scores of pain assessments such as score 0-3 where 0 is no response, 1 is slight movement, 2 is strong withdrawal, 3 is flinching - how do you input these scores?

Thank you so much for all your time and help!

[petersenpeter]

Hi Julia

Thanks for all your feedback and for attending the workshop! As promised, I have drafted schemas for your very standardized Von Frey tests and other behavioral tests and procedures. :-)

After further consideration, I suggest adding the Von Frey test as a subject log. There is no digital data collected; it mainly consists of observational logging. I have drafted three new subject logs: the Von Frey test, the Hargreaves test, and a Generic observation.

I also drafted new procedure types: Blood Pressure Sensor Implant, Breathing Sensor Implant, GRIN (Gradient Index) Lens Implant, ECG Implant (Electrocardiography), Nerve Cuff Implant, Temperature Sensor Implant, and a Generic Implant.

I would appreciate it if you could take some time to provide feedback on how well they cover your experiments. I will add them below as separate messages for better tracking of comments. Please let me know if the options provided are sufficient, if critical aspects of your procedures are described, and if you would like to save additional information.

[petersenpeter]

Von Frey test

• Stimulus location: Selection from below options:
  "Left hind paw",
  "Right hind paw",
  "Left forepaw",
  "Right forepaw",
  "Face (left)",
  "Face (right)",
  "Tail",
  "Other",
  (description: Anatomical location where the Von Frey filament was applied.)

• Stimulus force (g): number, min 0 (description: Force of the Von Frey filament used for mechanical stimulation, in grams.)

• Response score (0–3): min 0, max 3. integer (description: Categorical assessment of behavioral response to stimulation. 0: No response, 1: Slight movement, 2: Strong withdrawal, 3: Flinching or escape)

• Repetitions: integer, min 0, default 10. (description: Number of repetitions of Von Frey stimulation at the given location)

[petersenpeter]

Hargreaves Thermal sensitivity test

• Stimulus location: select from below options:
  "Left hind paw",
  "Right hind paw",
  "Left forepaw",
  "Right forepaw",
  "Face (left)",
  "Face (right)",
  "Tail",
  "Other",
  Description: Anatomical location where the thermal stimulus was applied using the Hargreaves test
• Withdrawal latency (s): number, min 0, description: Time from stimulus onset to paw withdrawal, measured in seconds.
• Cutoff latency (s): number, min 0, description: Maximum allowable latency before automatic termination to prevent tissue damage
• Response score (0–3), integer, min 0, max 3, description: Categorical assessment of behavioral response. 0: No response, 1: Delayed movement, 2: Normal withdrawal, 3: Exaggerated or escape behavior
• Repetitions: integer, description: Number of repeated Hargreaves trials at the given location

[vncntprvst]

Hi Peter.
I would also add Face left / right for this test, similar to von Frey.
Thanks

[petersenpeter]

Great. I will add these options.

[petersenpeter]

Generic Observation

• Observation type: select from below options:
  "Pain score",
  "Grooming",
  "Exploration",
  "Freezing",
  "Facial expression",
  "Unusual behavior",
  "Other",
  description: The category or behavioral domain of the observation.
• Observation: string, description: Description of the observed behavior.
• Repetitions: integer, min 1, description: How many times this observation was recorded under the same condition.

[petersenpeter]

Blood Pressure Sensor Implant

• Sensor type: select from options: "telemetric", "catheter-based", "fluid-filled", "fiber-optic", "other",
  Description: Type of blood pressure sensor used
• Implant site: select from options below:
  "Femoral artery",
  "Carotid artery",
  "Aorta",
  "Ventral tail artery",
  "Left ventricle",
  "Subcutaneous (telemetry)",
  "Other"
  Description: Vascular or body location where the pressure sensor was implanted.
• Catheter material: select from options: "polyurethane", "silicone", "polyethylene", "PVC", "other"
  Anchoring method: select from options below:
  "suture", "tissue glue", "subcutaneous tunnel", "headcap", "other"
  Description: How the sensor and catheter were secured in place to prevent movement
• Signal transmission: select from options: "wireless", "tethered", "inductive", "optical", "other"
  Description: How the signal from the sensor is transmitted to the acquisition system.
• Sterilization method: Select from options: "Autoclave", "Ethylene Oxide", "Alcohol", "Gamma Irradiation", "None"
  Description: Sterilization technique used before implantation.

[petersenpeter]

Breathing Sensor Implant

• Sensor type: Select from options
  "Piezoelectric sensor",
  "Chest wall EMG",
  "Intranasal thermocouple",
  "Intranasal pressure sensor",
  "Tracheal airflow sensor",
  "Thoracic pressure sensor",
  "Plethysmography cannula",
  "Other"
  Description: Type of breathing sensor used.
• Implant site: Select from options
  "Chest wall",
  "Diaphragm",
  "Nasal cavity",
  "Trachea",
  "Pleural cavity",
  "Subcutaneous (telemetry)",
  "Other"
  Description: Anatomical location where the breathing sensor was implanted or attached.
• Wire or lead material: Select from options:
  "stainless steel",
  "silver",
  "silver chloride",
  "gold",
  "platinum",
  "nichrome",
  "tungsten",
  "flex cable",
  "other"
  Description: Material used for connecting wires or leads (if applicable).
• Anchoring method: Select from options:
  "sutured",
  "tissue glue",
  "subcutaneous tunnel",
  "cemented to skull",
  "headcap",
  "custom mount",
  "other"
  Description: How the sensor or wires were fixed in place during implantation.
• Signal transmission, Select from options:
  "tethered",
  "wireless",
  "telemetric",
  "inductive",
  "optical",
  "other"
  Description: Mode of signal transmission from the sensor to the acquisition device
• Sterilization method, select from options:
  "Autoclave",
  "Ethylene Oxide",
  "Alcohol",
  "Gamma Irradiation",
  "None"
  Description: Sterilization technique applied before implantation.

[petersenpeter]

ECG Implant

• Wire Count, integer, min 1.
• Wire Material, options: "stainless steel", "silver", "silver chloride", "gold", "platinum", "nichrome", "tungsten", "other"
• Wire Insulation Type, options: "Teflon", "polyimide", "silicone", "none", "other"
  Description: Insulation material covering the wire shaft, excluding the exposed recording tip.
• Implant site, string
  Description: Vascular or body location where the pressure sensor was implanted.
• Anchoring Method
  Options: "suture", "tissue glue", "subcutaneous tunnel", "headcap", "cemented to skull", "other"
  Description: How the ECG wires were fixed in place to prevent movement.
• Sterilization method
  Options: "Autoclave", "Ethylene Oxide", "Alcohol", "Gamma Irradiation", "None"
  Description: Sterilization technique used for ECG components

[petersenpeter]

Hi Vincent and Julia

I added the discussed procedures and subject logs. Let me know how they fit your requirements.

[vncntprvst]

Thanks Peter! We'll take a look and we will let you know.