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WIP (point annotations) #169

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@froyo-np froyo-np commented Jun 3, 2025 •
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What

  • mild cleanup in render-server regarding lifecycle resource mgmt.
  • some react-level helpers to reduce repetative boilerplate demo setup
  • refactor the ome-zarr slice renderer to handle volumetric data better (each layer may not have the same # of slices)
  • a decoder for neuroglancer precomputed annotation files
  • a renderer for points in the above file format
  • a janky demo of all of the above

How

Replace this txt describing what kind of technical overlaying code changes were introduced here.

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  • Hint : Drag and Drop any images you want to add to the PR. Also you can create a gif of an interactive version and add that!

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  • Is your PR title following our conventional commit naming recommendations?
  • Have you filled in the PR Description Template?
  • Is your branch up to date with the latest in main?
  • Do the CI checks pass successfully?
  • Have you smoke tested the example applications?
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froyo-np added 22 commits May 30, 2025 15:43
@froyo-np
first pass at implementing a decoder for ng-precomputed annotation files
e61c736
@froyo-np
a little fiddling to promote type safety when extracting these annota…
d17a40f 
…tions
@froyo-np
fill out a renderer system for this data type (points only for now)
3c26561
@froyo-np
first draft of one way of doing this
7c39e47
@froyo-np
Merge branch 'main' into noah/ng-annotations
7389252
@froyo-np
less copy pasta
3f0a46d
@froyo-np
Merge branch 'noah/ng-annotations' of https://github.com/AllenInstitu…
cd1a2f0 
…te/vis into noah/ng-annotations
@froyo-np
update omezarr render settings to be easier to use for "real" volumet…
26414bc 
…ric LOD pyramids - all our previous examples were really just collections of slices (eg, every layer in the ome-zarr had the same shape on the Z axis - eg. 142 slices).
@froyo-np
fix up handling of volumetric slicing. correct disparity between exam…
22b75f1 
…ple data being in different units
@froyo-np
fmt
ecf6256
@froyo-np
put the logger back
7a8cfdb
@froyo-np
Merge branch 'main' into noah/ng-annotations
98535c1
@froyo-np
lint
89c233f
@froyo-np
Merge branch 'noah/ng-annotations' of https://github.com/AllenInstitu…
4a6a8e0 
…te/vis into noah/ng-annotations
@froyo-np
lockfile
9b74b14
@froyo-np
fmt again
a830850
@froyo-np
Merge branch 'main' into noah/ng-annotations
4de0fd7
@froyo-np
missed a spot in the refactor
ac3d62e
@froyo-np
fmt
65baf43
@froyo-np
cleanup, fix the schema to match real data, rather than the documenta…
8ef0e44 
…tion of the format...
@froyo-np
fmt
b101c8a
@froyo-np
timewasters
1d96b5e
@froyo-np froyo-np marked this pull request as ready for review June 26, 2025 16:48
@froyo-np froyo-np requested a review from a team as a code owner June 26, 2025 16:48
@froyo-np froyo-np requested review from TheMooseman and suyli7 June 26, 2025 16:48
froyo-np
froyo-np commented Jun 26, 2025
View reviewed changes
packages/precomputed/src/loader/annotations.test.ts
const base =
'https://aind-open-data.s3.amazonaws.com/SmartSPIM_787715_2025-04-08_18-33-36_stitched_2025-04-09_22-42-59/image_cell_segmentation/Ex_445_Em_469/visualization/detected_precomputed/';
const expectedMetadata: AnnotationInfo<'point'> = {
annotation_type: 'point', // TODO: the real json files here use lowercase, wtf
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remove todo

froyo-np
froyo-np commented Jun 26, 2025
View reviewed changes
packages/precomputed/src/loader/annotations.ts
unit: data.dimensions[key][1] as NGUnit,
scale: data.dimensions[key][0],
}));
// TODO this is gross - but not quite as gross as it looks - make the schema nicer!
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todone

froyo-np
froyo-np commented Jun 26, 2025
View reviewed changes
site/src/examples/annotated/Demo.tsx
} as const;
const dots =
'https://aind-open-data.s3.amazonaws.com/SmartSPIM_787715_2025-04-08_18-33-36_stitched_2025-04-09_22-42-59/image_cell_segmentation/Ex_445_Em_469/visualization/detected_precomputed/';
function useJunk() {
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todo rename me

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@TheMooseman TheMooseman Awaiting requested review from TheMooseman TheMooseman is a code owner automatically assigned from AllenInstitute/app-dev

@suyli7 suyli7 Awaiting requested review from suyli7 suyli7 is a code owner automatically assigned from AllenInstitute/app-dev

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