Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

update some links #39

Merged
merged 2 commits into from
Mar 22, 2022
Merged

update some links #39

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
de5bf9f
update some links
mccalluc Mar 16, 2022
16cc7c0
Update README.md
mccalluc Mar 21, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 10 additions & 10 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,9 @@ Included as a submodule in [portal-ui](https://github.com/hubmapconsortium/porta

Data for the Vitessce visualization almost always comes via raw data that is processed by [ingest-pipeline](https://github.com/hubmapconsortium/ingest-pipeline) airflow dags.
Harvard often contributes our own custom pipelines to these dags that can be found in [portal-containers](https://github.com/hubmapconsortium/portal-containers).
The outputs of these pipelines are then converted into view configuration for Vitessce in the [portal backend](https://github.com/hubmapconsortium/portal-ui/tree/master/context/app/api/vitessce_confs) when a `Dataset` that should be visualized is requested in the client.
The view configurations are built using the [Vitessce-Python API](https://vitessce.github.io/vitessce-python/index.html).
The outputs of these pipelines are then converted into view configurations for Vitessce by the [portal backend](https://github.com/hubmapconsortium/portal-ui/blob/0b43a468fff0256a466a3bf928a83893321ea1d9/context/app/api/client.py#L165),
using code in this repo, when a `Dataset` that should be visualized is requested in the client.
The view configurations are built using the [Vitessce-Python API](https://vitessce.github.io/vitessce-python/).

### Imaging Data

Expand All @@ -23,7 +24,7 @@ Below are common questions and answers for imaging modalities:

If so, we should ask the TMC to follow the instructions below for viewing their data in Avivator to make sure it looks right (should only need to be done for a single representative file): https://github.com/hms-dbmi/viv/tree/master/tutorial

In the above instructions they should only need to a) run the bioformats2raw-raw2ometiff pipeline and then b) drag-and-drop or select the input file using the "CHOOSE A FILE" button on avivator.gehlenborglab.org. There is no need for a web server.
In the above instructions they should only need to a) run the `bioformats2raw-raw2ometiff` pipeline and then b) drag-and-drop or select the input file using the "CHOOSE A FILE" button on avivator.gehlenborglab.org. There is no need for a web server.

If there is a z or t stack to the data, ensure that each "stack" is uploaded as a single file.

Expand All @@ -41,22 +42,21 @@ If there is segmentation data coming from the TMC or elsewhere, then that will n
<details><summary>Will Cytokit + SPRM be run?</summary>

If the answer is "yes," we should run [sprm-to-anndata.cwl from portal-containers](https://github.com/hubmapconsortium/portal-containers/tree/master/containers/sprm-to-anndata) on the output of SPRM and the image pyramid pipeline + offsets on the output of Cytokit.
Attach the assay, if it is not automatically attached, in the portal backend to the `StitchedCytokitSPRMConf` class in [context/app/api/vitessce_confs/assay_confs.py](https://github.com/hubmapconsortium/portal-ui/blob/9b49abda02e4f0579590289fc476eab23fa4cb02/context/app/api/vitessce_confs/assay_confs.py#L257-L290)
Extend [`StitchedCytokitSPRMViewConfBuilder`](https://github.com/hubmapconsortium/portal-visualization/blob/d9e924547d970f8469cf74881ce05cc22500b7fc/src/builders/sprm_builders.py#L287) to handle this assay.
</details>

<details><summary>Will only SPRM be run (on non-Cytokit Segmentations)?</summary>

If the answer is "yes," we should run [sprm-to-anndata.cwl from portal-containers](https://github.com/hubmapconsortium/portal-containers/tree/master/containers/sprm-to-anndata) from portal-containers on the output of SPRM and the image pyramid pipeline + offsets on the raw input data.
Attach the assay to a new class in the portal backend similar to [StitchedCytokitSPRMConf](https://github.com/hubmapconsortium/portal-ui/blob/9b49abda02e4f0579590289fc476eab23fa4cb02/context/app/api/vitessce_confs/assay_confs.py#L171-L197) that wraps [SPRMAnnDataViewConfs](https://github.com/hubmapconsortium/portal-ui/blob/9b49abda02e4f0579590289fc476eab23fa4cb02/context/app/api/vitessce_confs/base_confs.py#L258-L313) in [context/app/api/vitessce_confs/assay_confs.py](https://github.com/hubmapconsortium/portal-ui/blob/9b49abda02e4f0579590289fc476eab23fa4cb02/context/app/api/vitessce_confs/assay_confs.py#L257-L290) if needed for multiple images in the same dataset.
Otherwise you may simply use SPRMAnnDataViewConfBuilder with the proper arguments.
Create a new class that extends `MultiImageSPRMAnndataViewConfBuilder`, similar to [`StitchedCytokitSPRMViewConfBuilder`](https://github.com/hubmapconsortium/portal-visualization/blob/d9e924547d970f8469cf74881ce05cc22500b7fc/src/builders/sprm_builders.py#L287) if needed for multiple images in the same dataset.
Otherwise you may use [`SPRMAnnDataViewConfBuilder`](https://github.com/hubmapconsortium/portal-visualization/blob/d9e924547d970f8469cf74881ce05cc22500b7fc/src/builders/sprm_builders.py#L138) with the proper arguments.
</details>

<details><summary>For everything else...</summary>

Run the image pyramid pipeline + offsets on the raw input data.
Attach the assay to a new class in the portal backend similar to SeqFISHViewConfBuilder or to the already existing ImagePyramidViewConfBuilder as needed in [context/app/api/vitessce_confs/assay_confs.py](https://github.com/hubmapconsortium/portal-ui/blob/9b49abda02e4f0579590289fc476eab23fa4cb02/context/app/api/vitessce_confs/assay_confs.py#L257-L290).
Attach the assay to a new class in the portal backend similar to [`SeqFISHViewConfBuilder`](https://github.com/hubmapconsortium/portal-visualization/blob/d9e924547d970f8469cf74881ce05cc22500b7fc/src/builders/imaging_builders.py#L113) or [`ImagePyramidViewConfBuilder`](https://github.com/hubmapconsortium/portal-visualization/blob/d9e924547d970f8469cf74881ce05cc22500b7fc/src/builders/imaging_builders.py#L58).
This will depend on how you want the layout to look to the end user.
See the [SeqFISHViewConfBuilder](https://github.com/hubmapconsortium/portal-ui/blob/9b49abda02e4f0579590289fc476eab23fa4cb02/context/app/api/vitessce_confs/assay_confs.py#L45-L95) for an example of how hairy this can get.
</details>

### Sequencing Data
Expand All @@ -70,8 +70,8 @@ Currently, `RNA-seq` data comes as `AnnData` `h5ad` files from [Matt's pipeline]
3. A filter for a subset of genes (corresponding to the marker genes) is stored so that it may be rendered as a heatmap.
4. Save this altered dataset as a `.zarr` store.

The steps for doing that are contained in a python script [here](https://github.com/hubmapconsortium/portal-containers/blob/dc568234c76017c7cd9644a4d15ef0f7b9d84e24/containers/anndata-to-ui/context/main.py#L17-L67) that is run after Matt's pipeline and the corresponding python visualization code for the portal backend is [here](https://github.com/hubmapconsortium/portal-ui/blob/9b49abda02e4f0579590289fc476eab23fa4cb02/context/app/api/vitessce_confs/assay_confs.py#L200-L238).
Currently the portal backend cannot handle `slide-seq`, which is a spatially resolved `RNA-seq` assay, but its `ViewConfBuilder` class will look identical to the other [`AnnData`-backed `RNA-seq` datasets](https://github.com/hubmapconsortium/portal-ui/blob/9b49abda02e4f0579590289fc476eab23fa4cb02/context/app/api/vitessce_confs/assay_confs.py#L200-L238), except for an additional `spatial_polygon_obsm="X_spatial"` argument to the `AnnDataWrapper` as well as a `SPATIAL` vitessce component in the view config.
These steps are exexuted by the [`anndata-to-ui`](https://github.com/hubmapconsortium/portal-containers/blob/dc568234c76017c7cd9644a4d15ef0f7b9d84e24/containers/anndata-to-ui/context/main.py#L17-L67) container that is run after Matt's pipeline; The view config is generated by [`RNASeqAnnDataZarrViewConfBuilder`](https://github.com/hubmapconsortium/portal-visualization/blob/d9e924547d970f8469cf74881ce05cc22500b7fc/src/builders/anndata_builders.py#L13).
Currently the portal backend cannot handle `slide-seq`, which is a spatially resolved `RNA-seq` assay, but its `ViewConfBuilder` class will look be the same as `RNASeqAnnDataZarrViewConfBuilder`, except for an additional `spatial_polygon_obsm="X_spatial"` argument to the `AnnDataWrapper` as well as a `SPATIAL` vitessce component in the view config.
mccalluc marked this conversation as resolved.
Show resolved Hide resolved

#### xxxx-ATAC-seq

Expand Down