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spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
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Link to raw data is not working #1937

Open mstemmer opened 3 years ago

mstemmer commented 3 years ago

Hi,

I was trying to work through the input data formatting and found that the links to the raw data to some of the sample datasets do not work. E.g.: s3://czi.starfish.data.public/browse/raw/20180820/merfish_u2os/ OR s3://spacetx.starfish.data.public/browse/raw/seqfish/

In order to better understand the entire process, it would be very helpful to have a look at these datasets and run the conversion locally. Did the link change or are the data not available anymore?

All the best, Manuel.

ankitbioinfo commented 3 years ago

Hi Manuel,

Have you got any progress to get the manual data. I am bit confused about the auxilliary data dots. How to get the reference dot image? I am kind of working on seqFISH pipeline. In the example blob detection does not work without reference image. Any Idea what is the problem?

sebgoti commented 2 years ago

Hey @ankitbioinfo, if you do not have the reference dot image, have you tried to do a projection of all the channels and use that as a reference? Also, it would be helpful if you could mention to which data from the tutorial you are referring to.