Add a z-stack to the demo/component about viv HOT 7 CLOSED

If we can find a dataset for this I'd be really happy to convert to zarr.

from viv.

Not sure how much time you have, but if you want to participate in the sprint, I think the codex data has it. We can chat if you want to stop by 319a

from viv.

Nils posted a dataset from 4DN:

https://data.4dnucleome.org/files-microscopy/4DNFI5RC3LNA/
https://data.4dnucleome.org/experiment-set-replicates/4DNESMWANQOC/#raw-files
https://omero.hms.harvard.edu/pathviewer/vanilla-viewer/975138/

from viv.

Hi, I'm not sure if this is the same issue, but it would be great to have Z and T sliders for 5D images.
E.g. https://hms-dbmi.github.io/vizarr?source=https%3A%2F%2Fs3.embassy.ebi.ac.uk%2Fidr%2Fzarr%2Fv0.1%2F6001240.zarr should have a Z-slider.

Thanks,
Will

from viv.

@will-moore I think the feature request is for https://github.com/hms-dbmi/vizarr and not the underlying Viv package.

Here are some examples with z-stacks:
http://avivator.gehlenborglab.org/?image_url=https://vitessce-demo-data.storage.googleapis.com/test-data/antigen_exprs.ome.tiff
http://avivator.gehlenborglab.org/?image_url=https://vitessce-demo-data.storage.googleapis.com/test-data/35451.ome.tif

from viv.

Thanks, I created an issue at hms-dbmi/vizarr#41

from viv.

P.S If you are looking for a "batteries included" viewer we can release Avivator as a package or you may look at Vitessce, i.e:

http://vitessce.io/?url=data%3A%2C%7B%22version%22%3A+%220.1.0%22%2C+%22layers%22%3A%5B%7B%22fileType%22%3A%22raster.json%22%2C%22name%22%3A%22raster%22%2C%22type%22%3A%22RASTER%22%2C%22url%22%3A%22data%3Atext%2Fplain%3Bcharset%3Dus-ascii%3Bbase64%2CeyJpbWFnZXMiOiBbeyJuYW1lIjogIlIwMDFfWDAwMl9ZMDA5Lm9tZS50aWZmIiwgInR5cGUiOiAi%5Cnb21lLXRpZmYiLCAidXJsIjogImh0dHBzOi8vYXNzZXRzLmh1Ym1hcGNvbnNvcnRpdW0ub3JnLzlk%5CnM2E5NDI1ZGFkNjY1ZWE4ZTI2ZjU1NGIyYTIzNDg2L291dHB1dC9leHRyYWN0L2V4cHJlc3Npb25z%5CnL29tZS10aWZmL1IwMDFfWDAwMl9ZMDA5Lm9tZS50aWZmP3Rva2VuPSIsICJtZXRhZGF0YSI6IHsi%5Cnb21lVGlmZk9mZnNldHNVcmwiOiAiaHR0cHM6Ly9hc3NldHMuaHVibWFwY29uc29ydGl1bS5vcmcv%5CnOWQzYTk0MjVkYWQ2NjVlYThlMjZmNTU0YjJhMjM0ODYvb3V0cHV0X29mZnNldHMvUjAwMV9YMDAy%5CnX1kwMDkub2Zmc2V0cy5qc29uP3Rva2VuPSJ9fV0sICJzY2hlbWFWZXJzaW9uIjogIjAuMC4yIn0%3D%22%7D%2C%7B%22fileType%22%3A%22cells.json%22%2C%22name%22%3A%22cells%22%2C%22type%22%3A%22CELLS%22%2C%22url%22%3A%22https%3A%2F%2Fassets.hubmapconsortium.org%2F9d3a9425dad665ea8e26f554b2a23486%2Foutput_json%2FR001_X002_Y009.cells.json%3Ftoken%3D%22%7D%2C%7B%22fileType%22%3A%22cell-sets.json%22%2C%22name%22%3A%22cell-sets%22%2C%22type%22%3A%22CELL-SETS%22%2C%22url%22%3A%22https%3A%2F%2Fassets.hubmapconsortium.org%2F9d3a9425dad665ea8e26f554b2a23486%2Foutput_json%2FR001_X002_Y009.cell-sets.json%3Ftoken%3D%22%7D%2C%7B%22fileType%22%3A%22clusters.json%22%2C%22name%22%3A%22expression-matrix%22%2C%22type%22%3A%22EXPRESSION-MATRIX%22%2C%22url%22%3A%22https%3A%2F%2Fassets.hubmapconsortium.org%2F9d3a9425dad665ea8e26f554b2a23486%2Foutput_json%2FR001_X002_Y009.clusters.json%3Ftoken%3D%22%7D%5D%2C%22name%22%3A%22R001_X002_Y009%22%2C%22staticLayout%22%3A%5B%7B%22component%22%3A%22layerController%22%2C%22h%22%3A4%2C%22w%22%3A3%2C%22x%22%3A0%2C%22y%22%3A0%7D%2C%7B%22component%22%3A%22description%22%2C%22h%22%3A2%2C%22w%22%3A3%2C%22x%22%3A0%2C%22y%22%3A4%7D%2C%7B%22component%22%3A%22cellSets%22%2C%22h%22%3A4%2C%22w%22%3A2%2C%22x%22%3A10%2C%22y%22%3A2%7D%2C%7B%22component%22%3A%22genes%22%2C%22h%22%3A2%2C%22props%22%3A%7B%22variablesLabelOverride%22%3A%22antigen%22%7D%2C%22w%22%3A2%2C%22x%22%3A10%2C%22y%22%3A0%7D%2C%7B%22component%22%3A%22heatmap%22%2C%22h%22%3A2%2C%22props%22%3A%7B%22transpose%22%3Atrue%2C%22variablesLabelOverride%22%3A%22antigen%22%7D%2C%22w%22%3A7%2C%22x%22%3A3%2C%22y%22%3A4%7D%2C%7B%22component%22%3A%22spatial%22%2C%22h%22%3A4%2C%22props%22%3A%7B%22view%22%3A%7B%22target%22%3A%5B600%2C600%2C0%5D%2C%22zoom%22%3A-1.5%7D%7D%2C%22w%22%3A7%2C%22x%22%3A3%2C%22y%22%3A0%7D%5D%7D&theme=dark

from viv.