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# Status updates on the Prototype of the CEMBA web portal
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***from March 13, 2019 CEMBA Biweekly Meeting***
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## :goal: Goals
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* [ ] Use tabular data to identify the available projections of TRIO tracing.
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* [ ] Use CCFv3, Marga drawings, and ARA to identify and visualize the contrast of regions of interests.
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* [ ] Provide entry points to molecule data (Eran’s group portal) and anatomy data (Hongwei’s group portal).
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---
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## :gear: UI Components
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* [ ] 🧠 Projections table of the TRIO tracing (EnvA Rabies, AAV2retro)
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* [ ] 🧠 ARA images
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* Levels (39, 46, 51)
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* [ ] 🧠 CCF images and Marga drawings
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* Slices (3, 4, 5)
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* Drawings (3A~3F, 4A~4H, 5A~5J)
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**💉TRIO tracers**
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```
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* Env Rabies
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* EnvA G-deleted rabies RVdG-4mCherry
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* AAV8-hSyn-FLEX-TVA-P2A-GFP-2A-oG
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* AAV (AAV2retro)
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* AAVretro-EF1a-Cre
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```
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*TRIO tracing table of projected regions.*
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<hr><br><br><br>
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*ARA Level 39 / CEMBA CCF Slice 3 and Marga drawings (3A~3F)*
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<hr><br><br><br>
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*ARA Level 46 / CEMBA CCF Slice 4 and Marga drawings (4A~4H)*
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<hr><br><br><br>
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*ARA Level 51 / CEMBA CCF Slice 5 and Marga drawings (5A~5J)*
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<br><br>
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---
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## :link: Link
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*X (marked as projection is present), will give an user an option to jump*
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<br><br><br>
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*Data Repository of our published cases (Dashboard page)*
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<br><br><br>
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*Gene methylation portal (Brainome portal)*
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<br><br><br>
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---
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## :robot: Run
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---
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## :fearful: Feedbacks
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:pencil:
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>
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Fixing an ARA level for CCF v3 is misleading because the dissected blocks (Marga Drawing’s) are volumes. (50μm vs 600μm)
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>
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:pencil:
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Perhaps pick the levels for corresponding blocks and the user can select the levels. And choose the middle level from that range.
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>
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:pencil:
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>
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Sagittal image and show the corresponding levels.
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>
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:pencil:
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>
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Use new (Nissl/CCF/Marga Drawings) images. https://www.dropbox.com/s/kxhmlb16ju0ycgl/CEMBA_MargaDrawings_AllSlices.pptx?dl=0
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>
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:pencil:
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>
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Information on what atlas images are used, name, and version. i.e.) ARA, CCF v3, etc..
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>
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:pencil:
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Warning or clear label that states that the dissections were performed based on CCF.
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>
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---
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### 🤯 Something to think about
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🅿
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>
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* Problem 1: Connectivity data uses ARA not CCF v3
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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.)
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>
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🅿
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>
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* 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.
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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).
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>
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🅿
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>
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* 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.
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Click on CCF v3 on a ROI will highlight multiple corresponding regions on ARA. e.g.) Click on MOp should highlight MOp, SSp,
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>
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*ARA Level 39 and Marga Drawings from CCF Slice 3*
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### :desktop: Next steps
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*Next version of the UI*
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*Sagittal view image*
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#### *A positive comments from a CEMBA member*
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>>>
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### :stars: *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”.*
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### :stars: *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).*
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>>>
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**** |
