Closed giovp closed 4 months ago
Looks like there is a CODEX dataset we can get without having to wait on a rep: https://portal.hubmapconsortium.org/browse/dataset/053544cd63125fc25f6a71a8f444bafc#files
@LucaMarconato could you post the link to the metaspace and the nanostring geomx that you had in mind?
Here is a cool 3D single-molecule dataset with time information and multiple samples (multiple coordinate spaces) and paired with images. It would benefit from our infrastructure for deep learning applications. It's some GB so we need to subsample. The single-molecule data can be downloaded from here (link found in this paper). The associated images are not public (will be soon), but for the moment we will have access privately.
2 datasets from Resolve: Mouse skin (melanoma) - from this publication: https://www.nature.com/articles/s41586-022-05242-7 Data available here: https://zenodo.org/record/6856193#.Yzr3H3ZByF5
Mouse and human liver – from this publication: https://www.cell.com/cell/fulltext/S0092-8674(21)01481-1? Data available here: https://cloud.irc.ugent.be/public/index.php/s/HrXG9WKqjqHBEzS
Serial sections (i.e., multiple slides of the same sample) with different immunofluorescence techniques applied: https://mcmicro.org/datasets/#whole-slide-images-wsis
I haven't opened it, but based on the description I think it also comes with registration transformations, segmentation masks and measurements. Might be a nice example.
Additional info: https://www.synapse.org/#!Synapse:syn24849819/wiki/608441
edit: preview of the data with a browser-based viewer (minerva): https://labsyspharm.github.io/mcmicro-images/
Lightseq - sequencing + imaging
https://www.nature.com/articles/s41592-022-01604-1#data-availability
@kevinyamauchi, more resources (including notebooks for handling raw data) from their website: lightseq.io
Use case 1:
Use case 2:
Use case 3 (using 4 datasets):
Nice dataset and study from our colleagues at EBI and DKFZ: base-specific in situ sequencing (BaSISS), for studying clonal evolution in breast cancer
hey all- I'm excited to learn about this SpatialData
project and see the progress!
It looks like the readme.MD
refers to the MERSCOPE data as being from the Zhuang lab, but the download code here shows it grabbing the VISp data from our prototype MERFISH pipeline. It's fine to use this if you want, but
Thank you @berl we are working for making a beta release the soonest!
I have updated the README.md with the correct data attribution, sorry for that. And thank you for pointing us to the datasets you mentioned.
Thanks for catching the misattribution, @berl . Sorry about that!
it's a bit of an orphan dataset in terms of formatting, technical details, etc. upcoming BICCN Zhuang lab data or Allen Institute MERSCOPE data will be more useful long term.
Do you know when/where those datasets will be released? I'd be interested in checking them out.
Curio (commercialized slideseq) has example data upon request. It could be worth making a reader if we can get some of the data.
Closing, enough datasets added.
Available datasets
Missign datasets