Virtual Observatory of the Cortex

A BRAIN initiative funded U24 project to bring the IARPA MICrONS dataset to the scientific research community.

Is there an observation you could make from this dataset that would help you answer a scientific question, but you aren’t sure how to make it? Or maybe you know how to make it, but don’t have the time or resources to repair or annotate enough examples to answer your question.

The Virtual Observatory of the Cortex is a grant funded mechanism designed to assist you in precisely this situation. We provide the labor and experience to make corrections and annotations in the data. The results of these efforts will be integrated with an evolving version of the dataset, and shared with you and the larger scientific community.

We think of it as a metaphor for a large scale astronomy survey: we are providing the infrastructure and focusing mechanisms, the community is steering the observations to the spots of maximum interest, and everyone can see what comes out!

How it works

  • The scientific community submits a short request for information they believe might be contained within this dataset, but might require some work to extract. For example: proofreading axons and dendrites for a specific group of neurons; or annotating the locations of dense core vesicles in these particular cells; or that locations where microglia have engulfed synapses are annotated.

  • A scientist at the Allen Institute will work with you on developing a plan that helps address the scientific question you are interested in, including any manual proofreading and annotation work that needs to be done. Plans will be designed to maximize impact across all requests when possible.

  • A scientific steering committee will evaluate all the plans and prioritize the manual work based upon the resources available to the virtual observatory. Plans will then be carried out by staff of the virtual observatory, with no costs to the requestor.

  • The data produced from the efforts of the manual proofreaders is then shared with the entire scientific community for everyone to benefit from. Data releases will occur at least quarterly.

Tip: if you have a general question about the accessing the data, or bugs to report, contact the MICrONS team at info@microns-explorer.org.

Scientific Request Form

Please use the following form to indicate your interest in using the virtual observatory. The description of your scientific question can be brief and we will follow up with you via e-mail to understand it in more detail.

The demographic information is required for reporting to the NIH on the use of the resource and will only be shared in aggregated form.

 

Data Sharing Policy

Data created by the Vortex project, such a proofreading and annotations, will be integrated into broader publicly available dataset for everyone to use. Proofreading updates the segmentation, which will be released along with any other changes that are part of the centralized dataset, no matter their source. Annotations will be made on the dataset and released as tables via the CAVEclient, and periodically as static file dumps available via google cloud. See the specific dataset pages for details on data access.

Data Releases

 

  • Our quarterly data release includes:

    • Axon extension on 273 wholly new pyramidal cells, and upgrades to 400 previously proofread but truncated cells

    • Manual labeling of 20,000 synapse targets.

    See: v1181 Release Manifest for more

  • We have concluded our first Project Period, with:

    • Axon extension on 109 functionally co-registered pyramidal cells (6 previously proofread with incomplete extension, 103 wholly new).

    • Manual labeling of 73,000 synapse targets from 20 basket cells (putative parvalbumin cells).

    • Manual annotation of myelination and nodes of Ranvier on 53 mm of axon.

    • Selection of 12 astrocytes for segmentation quality and completeness, and ‘cleaning’ to remove incorrectly merged neurites from 3 astrocytes.

    See: v1078 Release Manifest for more

  • Highlights include: derived visual tuning properties of the functional recordings, associated with the coregistered cells. And updated flat segmentation.

  • Release of public datastack v795. Adds annotation tables containing the updated cell typing and models based on multiple methods, and further proofreading of various cell types including L5ET and L5IT excitatory cells.

    Public annotation tables can be viewed with the Dash App and the current segmentation explored with neuroglancer.

    Follow instructions in Visualization for data access

  • This released focused on releasing and updated version of the segmentation with more proofreading, including 1,051 cells with at least cleaned axons. It also marked the first release where almost 100% of the neurons have been made single soma. It also contained more co-registration, including a manual table with 13,925 entries, and a larger automated registration with >20,000 entries that had high confidence. Finally, the release contained updated cell type calls and models based on multiple methods.

    This release was accompanied by an update to the preprint describing the dataset (https://www.biorxiv.org/content/10.1101/2021.07.28.454025v3)

  • This version has an updated segmentation, which included more proofread cells including cells with at least clean 410 axons. It also contained an update to functional coregistration which includes now 9518 coregistered ROIs. Finally, it now includes a broader array of cell type calls in the dataset, including both manual and automated tables.

  • This was the initial release of the dataset, that included all the image data, the synapse detection, nucleus detection, and the functional dataset. It included 249 cells with at least clean dendrites, and 200 functional coregistered cells. It had some basic cell type calls including a model for what was likely neurons in the dataset, and excitatory vs inhibitory calls, both manual and automated.

 

Current Efforts

Exploration of functional circuits

Investigating the reciprocal connectivity and the functional organization on inputs on their dendritic tree, to understand the input-output computations that determine the visual tuning of cortical neurons.

--F. Rossi, H.N Strelevitz

Testing a computational theory that that dendritic spine neck coupling is related to the degree of correlation between the inputs to that synapse with its dendritic neighbor synapses.

--C. O’Donnell

Investigating whether feedforward and feedback interareal-projecting neurons are selectively wired in closed loops, that is to say reciprocally connected at the population or cell-to-cell level.

--L. Petreanu

Proofreading efforts: extending the axons of coregistered neurons (excitatory neurons that have in vivo imaging)

Astrocyte anatomy

Quantitative characterization of astrocyte anatomy, in furtherance of a digital twin model

--M. de Pitta, Z. Sun

Proofreading efforts: inspecting and repairing the segmentation of representative astrocytes

Identifying long-range inhibitory cells

Reconstructing the axons of a unique population of long-range projecting inhibitory neurons in the neocortex, to determine the local inputs and outputs.

--R. Batista-Brito, J. Ratliff

Proofreading efforts: surveying inhibitory cells for axons in white matter; extending putative chodl cell axons

Connectivity and annotation of parvalbumin interneuron

A cell-type deep dive into putative parvalbumin (PV) interneurons, looking specifically at features of their connectivity—both inputs and outputs—and myelination.

--K. Micheva

Proofreading efforts: 1) annotate inhibitory synapses for whether the target is spine or non-spine, 2) annotate the presence of myelin along the axon, 3) annotate putative thalamocortical inputs onto basket cells

Vasculature

Modeling the effect of vasculature on the distribution of electric charge due to an applied electric field (brain stimulation).

--G. Noetscher, S. Makaroff

Investigating the mechanism of neuro-vascular coupling, whether through astrocytic endfeet or direct neurotransmission.

-- D. Kleinfeld, A. Shih, J. How

Proofreading efforts: generation of a cleaned vasculature mesh layer

Previous Efforts

Description of previous proofreading/annotation projects with number of edits with links and/or graphs/pictures if applicable.