spacetx / sptx-format Goto Github PK
View Code? Open in Web Editor NEWImage data format specification for spaceTx
License: MIT License
Image data format specification for spaceTx
License: MIT License
use, e.g., MANIFEST.IN with include_package_data
Change hybridization images to primary images. Propagate these changes through the other repositories, potentially through creating constants in this package that are importable.
need a plan that states how we will increment versioning.
@hewgreen suggested that HCA metadata has outlawed the type of implicit linking we have in our specification.
Example experiment.json
{
hybridization_images: "hybridization.json",
...,
}
In existing specification, we link a file which is implicitly of a particular type. Here it can be either an fov_manifest.json
or a field_of_view.json
.
HCA metadata suggests making it an explicit link, wherein it should contain the metadata structure. Investigate the pros/cons of this for our use cases.
move primary_images validation to slicedimage
The schema claims that it is ordered (x, y)
https://github.com/spacetx/sptx-format/blob/master/schema/field_of_view/field_of_view.json#L91
Internally, we don't validate on this field yet, we simply slurp in the data and make sure that the sizes fit. However, we might want to provide information on a TileSet (before it's loaded into memory).
We should replace this with an explicit map of {x: size, y: size}
, instead of a list to prevent errors.
Starfish constants should live here so that they are only updated in one repo.
Implementation possibilities include:
Jinja
template json schema that are rendered by CIWe should have a validator for spaceTx format so that we can:
We should lift some of the prose from the below document and update it into a README that can be provided to spaceTx collaborators.
https://docs.google.com/document/d/12V-BQF-wh1GDBXwUH2hQrPhw6n0oQqENPK-YHGv59w4/edit#
The codebook should associate information about the channel ID with the channel indices to enable user-driven QC.
Codebook is currently unversioned.
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