allow for datasets queries based on brain regions, and number of neurons recorded?

[duutabib]

I am interested in datasets of neural populations (~10K neurons) from different brain regions. However, I am unable to query at that resolution using your tools, or am I missing something?

Thanks kindly in advance.

[CodyCBakerPhD]

I am interested in datasets of neural populations (~10K neurons) from different brain regions.

If you mean simultaneous recordings of that many neurons+regions, your best best would be to search for 'whole brain microscopy' which has a couple of datasets on that scale

Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior: Number of ROIs (neurons and/or glia) on the order of hundreds of thousands, but very low temporal resolution

Thermoregulatory Responses Midbrain + Hindbrain: similar in style/scale to the glia one, but each dataset is specific to the subregions

If on the other hand, you're OK with the cells not being detected simultaneously but instead being observed in different sessions with different subjects (different regions each time) then you should definitely check these two out

IBL - Brain Wide Map

Mesoscale Activity Map Dataset

However, I am unable to query at that resolution using your tools, or am I missing something?

Improved search UI is something we're actively working on - what kind of search tool would you envision for helping discover datasets like this?

[duutabib]

Hello Cody,

Many thanks for your quick response. I will have a look into these. I am actually interested in simultaneous recordings of ROIs from different regions ideally in spontaneous activity states.

I envision a UI that allows one to query along these lines individually and simultaneously. For example, filter based on number of ROIs, state of the brain, region of the brain etc. I'd imagine such datasets are already available but, the absence of standardization of descriptors might make it difficult for one to find these datasets.

I will like to thank you again, and will let you know there are any challenges as I plow along.

Best wishes, Duut.Abib ------------------------------------------------------------------------------------------------------

On Fri, Aug 4, 2023 at 6:28 AM Cody Baker @.***> wrote:

I am interested in datasets of neural populations (~10K neurons) from different brain regions.

If you mean simultaneous recordings of that many neurons+regions, your best best would be to search for 'whole brain microscopy' which has a couple of datasets on that scale

Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior https://dandiarchive.org/dandiset/000350: Number of ROIs (neurons and/or glia) on the order of hundreds of thousands, but very low temporal resolution

Thermoregulatory Responses Midbrain https://dandiarchive.org/dandiset/000236 + Hindbrain https://dandiarchive.org/dandiset/000237: similar in style/scale to the glia one, but each dataset is specific to the subregions

If on the other hand, you're OK with the cells not being detected simultaneously but instead being observed in different sessions with different subjects (different regions each time) then you should definitely check these two out

IBL - Brain Wide Map https://dandiarchive.org/dandiset/000409

Mesoscale Activity Map Dataset https://dandiarchive.org/dandiset/000363/0.230613.1608

However, I am unable to query at that resolution using your tools, or am I missing something?

Improved search UI is something we're actively working on - what kind of search tool would you envision for helping discover datasets like this?

— Reply to this email directly, view it on GitHub https://github.com/dandi/helpdesk/issues/112, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACZWKPA3XX2KVZ73EKYD64LXTSB6HANCNFSM6AAAAAA3CSDACE . You are receiving this because you authored the thread.Message ID: @.***>

[duutabib]

Hello Cody,

For IBL datasets, I am having a challenge accessing passivePeriods for some datasets, any chance you could help me with that?

Best wishes, Duut.Abib ------------------------------------------------------------------------------------------------------

On Mon, Aug 7, 2023 at 10:39 AM Abib Duut @.***> wrote:

Hello Cody,

Many thanks for your quick response. I will have a look into these. I am actually interested in simultaneous recordings of ROIs from different regions ideally in spontaneous activity states.

I envision a UI that allows one to query along these lines individually and simultaneously. For example, filter based on number of ROIs, state of the brain, region of the brain etc. I'd imagine such datasets are already available but, the absence of standardization of descriptors might make it difficult for one to find these datasets.

I will like to thank you again, and will let you know there are any challenges as I plow along.

Best wishes, Duut.Abib

------------------------------------------------------------------------------------------------------

On Fri, Aug 4, 2023 at 6:28 AM Cody Baker @.***> wrote:

I am interested in datasets of neural populations (~10K neurons) from different brain regions.

If you mean simultaneous recordings of that many neurons+regions, your best best would be to search for 'whole brain microscopy' which has a couple of datasets on that scale

Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior https://dandiarchive.org/dandiset/000350: Number of ROIs (neurons and/or glia) on the order of hundreds of thousands, but very low temporal resolution

Thermoregulatory Responses Midbrain https://dandiarchive.org/dandiset/000236 + Hindbrain https://dandiarchive.org/dandiset/000237: similar in style/scale to the glia one, but each dataset is specific to the subregions

If on the other hand, you're OK with the cells not being detected simultaneously but instead being observed in different sessions with different subjects (different regions each time) then you should definitely check these two out

IBL - Brain Wide Map https://dandiarchive.org/dandiset/000409

Mesoscale Activity Map Dataset https://dandiarchive.org/dandiset/000363/0.230613.1608

However, I am unable to query at that resolution using your tools, or am I missing something?

Improved search UI is something we're actively working on - what kind of search tool would you envision for helping discover datasets like this?

— Reply to this email directly, view it on GitHub https://github.com/dandi/helpdesk/issues/112, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACZWKPA3XX2KVZ73EKYD64LXTSB6HANCNFSM6AAAAAA3CSDACE . You are receiving this because you authored the thread.Message ID: @.***>

[CodyCBakerPhD]

The IBL passive data release is still in progress as far as I know, so it hasn't made its way over to DANDI yet

Last correspondence I had with them on the matter noted a new release by the end of the year

[duutabib]

I will brute force it then. Many thanks Cody. I will be in touch if I have any other questions.

Going back to comments on the UI: https://knowledge.brain-map.org/data?limit=25&offset=0&sort=species.name~ASC https://knowledge.brain-map.org/data?limit=25&offset=0&sort=species.name~ASC have something along the lines I was thinking, although it doesn't account for brain states (example: spontaneous activity). I hope this makes things clearer.

Do have a nice day!

Best wishes, Duut.Abib ------------------------------------------------------------------------------------------------------

On Mon, Aug 7, 2023 at 10:43 PM Cody Baker @.***> wrote:

The IBL passive data release https://int-brain-lab.github.io/iblenv/notebooks_external/loading_passive_data.html#Loading-Passive-Data is still in progress as far as I know, so it hasn't made its way over to DANDI yet

Last correspondence I had with them on the matter noted a new release by the end of the year

— Reply to this email directly, view it on GitHub https://github.com/dandi/helpdesk/issues/112, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACZWKPBNKRVHKUEV7VO2AZ3XUFOQPANCNFSM6AAAAAA3CSDACE . You are receiving this because you authored the thread.Message ID: @.***>