cemba prototype

Status updates on the Prototype of the CEMBA web portal

from March 13, 2019 CEMBA Biweekly Meeting

🥅 Goals

Use tabular data to identify the available projections of TRIO tracing.
Use CCFv3, Marga drawings, and ARA to identify and visualize the contrast of regions of interests.
Provide entry points to molecule data (Eran’s group portal) and anatomy data (Hongwei’s group portal).

⚙ UI Components

🧠 Projections table of the TRIO tracing (EnvA Rabies, AAV2retro)
🧠 ARA images
- Levels (39, 46, 51)
🧠 CCF images and Marga drawings
- Slices (3, 4, 5)
- Drawings (3A~3F, 4A~4H, 5A~5J)

💉TRIO tracers

* Env Rabies
  * EnvA G-deleted rabies RVdG-4mCherry
  * AAV8-hSyn-FLEX-TVA-P2A-GFP-2A-oG
* AAV (AAV2retro)
   * AAVretro-EF1a-Cre

TRIO tracing table of projected regions.

ARA Level 39 / CEMBA CCF Slice 3 and Marga drawings (3A~3F)

ARA Level 46 / CEMBA CCF Slice 4 and Marga drawings (4A~4H)

ARA Level 51 / CEMBA CCF Slice 5 and Marga drawings (5A~5J)

🔗 Link

X (marked as projection is present), will give an user an option to jump

Data Repository of our published cases (Dashboard page)

Gene methylation portal (Brainome portal)

🤖 Run

😨 Feedbacks

📝

Fixing an ARA level for CCF v3 is misleading because the dissected blocks (Marga Drawing’s) are volumes. (50μm vs 600μm)

📝

Perhaps pick the levels for corresponding blocks and the user can select the levels. And choose the middle level from that range.

📝

Sagittal image and show the corresponding levels.

📝

Use new (Nissl/CCF/Marga Drawings) images. https://www.dropbox.com/s/kxhmlb16ju0ycgl/CEMBA_MargaDrawings_AllSlices.pptx?dl=0

📝

Information on what atlas images are used, name, and version. i.e.) ARA, CCF v3, etc..

📝

Warning or clear label that states that the dissections were performed based on CCF.

🤯 Something to think about

🅿

Problem 1: Connectivity data uses ARA not CCF v3 Use the hybrid of Nissl/CCF v3 and provide the user with the ability to switch non-Nissl side of the image. (Nissl, raw data, is independent from any atlas.)

🅿

Problem 2: Marga’s dissected tissue regions don’t necessarily single out one ROI. i.e.) MOp is not necessarily MOp, it’s MOp and SSp. Show both the front and back (anterior and posterior surface) for each region; ideally, you could also show all the intermediate levels (as a gallery or by allowing the user to click through the levels).

🅿

Problem 3: Warped dissected tissue regions atop ARA does not look good and visually distorted because CCF v3 is wider than ARA to register on top of ARA. Click on CCF v3 on a ROI will highlight multiple corresponding regions on ARA. e.g.) Click on MOp should highlight MOp, SSp,

ARA Level 39 and Marga Drawings from CCF Slice 3

🖥 Next steps

Next version of the UI

Sagittal view image

A positive comments from a CEMBA member

🌠 We can separate the issues of “What was collected” (i.e. the drawing of the shape of Marga’s dissection and corresponding Nissl image) from “What brain region/nomenclature/annotation is it”.

🌠 I think it could be really valuable to show both annotations (CCF3 and ARA) or give the user the option to select which one to view. In fact, I think that would be a valuable tool in general for the community (independent of our data).

GitLab