Example image data for dask-image
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Description
### dask-image example datasets
We need some good example data for tutorials with dask-image.
This issue is a place for discussion and suggestions. If you have links, add them here!
Ideally this data should:
* Have a permissive license
* Be easily downloaded on demand by the user
* Be big, but not too big. We want something that will automatically be spread over a few dask chunks, but not too large to download. 1 - 2 GB? What makes sense here?
It would be nice to have
* scientific images (microscopy, astronomy, satellite/geo-spatial images, maybe histology slides)
* a filetype we don't need another third party library to open (we have pims already, something it could handle would be ideal)
* the data hosted by someone else, but in a stable situation where we can reasonably count on that continuing
What we want to avoid:
* Websites that make you register (even for free) before you can download data.
EDIT:
https://github.com/napari/napari/issues/316
> Just saw this tweet announcing a human brain MRI at 100µm isotropic resolution. This could be a very cool dataset to use as a napari demo. I suggest we use this issue to keep track of datasets that we could put in napari once we have proper data downloading. Please just edit the checklist below to add your preferred demo data.
>
> * [ ] 100µm resolution human brain: https://twitter.com/ComaRecoveryLab/status/1134436231775961088
>
> * [ ] 10m resolution vegetation cover in Victoria: http://francois-petitjean.com/Research/MonashVegMap/info.php and https://labo.obs-mip.fr/multitemp/mapping-a-part-of-australia-at-10-m-resolution/
>
> * [ ] correlative superres https://www.biorxiv.org/content/10.1101/773986v1.abstract
>
> * [x] SARS-CoV2 in gut epithelium https://twitter.com/notjustmoore/status/1256232842755014656
>
> * [ ] developing sea squirt https://www.nytimes.com/2020/07/09/science/sea-squirts-embryos.html
>
> * [ ] mechanobiology of intestinal organoids https://twitter.com/XavierTrepat/status/1308026944349450241
>
> * [ ] tracking of particles on astral microtubules ([paper](https://www.biorxiv.org/content/10.1101/2020.06.17.154260v1), [tweet (😍)](https://twitter.com/the_Node/status/1341050276011237379)), could make a really neat demo for the tracks layer.
>
> * [ ] [Sentinel-2 1y Cloud optimised geotiff dataset](https://medium.com/sentinel-hub/digital-twin-sandbox-sentinel-2-collection-available-to-everyone-20f3b5de846e)
>
> * [ ] Calcium imaging in the Drosophila ellipsoid body ([2013](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3830704/) and [2015](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704792/))
>
> * [ ] Janelia FlyLight data ([AWS](https://registry.opendata.aws/janelia-flylight/))
>
> * [ ] Fruit Fly Brain Observatory (FFBO) ([tweet](https://twitter.com/FlyBrainObs/status/1369496338266750977))
>
> * [ ] Janelia [Open Organelle datasets](https://openorganelle.janelia.org/)
>
> * [ ] CZBiohub [Open Cell](https://opencell.czbiohub.org/about)
>
> * [ ] [CoCo](https://cocodataset.org/#download) + [Voxel51 datasets](https://voxel51.com/docs/fiftyone/user_guide/using_datasets.html)
>
> * [ ] @tlambert03's lattice light sheet dataset used in the dask application post https://www.ebi.ac.uk/biostudies/studies/S-BSST435?query=Talley%20lambert
> two cryo-ET datasets to add to the pile
>
> * https://zenodo.org/record/6504891 - deconvolved tomogram of HIV virus-like particles + annotations
> * https://zenodo.org/record/6504949 - denoised tomogram of a M. pneumonaie cell
> There is also some more developing Tribolium embryos, mouse brain slices and mouse colon volumes:
>
> https://zenodo.org/record/4276076#.YYJKMWDMJaR
https://github.com/napari/napari/issues/316#issuecomment-952642188
> ... and this 3D cell tracking dataset is gorgeous! http://celltrackingchallenge.net/
>
>> C.elegans developing embryo
>> Waterston Lab, University of Washington, Seattle, WA, USA
>> Training dataset: [http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DH-CE.zip✱](http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DH-CE.zip%E2%9C%B1) (3.1 GB)
>> Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-N3DH-CE.zip (1.7 GB)
>>
>> Microscope: Zeiss LSM 510 Meta
>> Objective lens: Plan-Apochromat 63x/1.4 (oil)
>> Voxel size (microns): 0.09 x 0.09 x 1.0
>> Time step (min): 1 (1.5)
>> Additional information: Nature Methods, 2008
Contributor guide
Research direction
No repository files, tests, or entry points are named. Review the proposed dataset links and the dask-image tutorial requirements first; the work is done only when a suitable, permissively licensed, downloadable dataset is selected and its tutorial use is agreed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data, documentation
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100