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Tutorial "Loading ImageJ ROI Sets" #1899

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giovp opened this issue Jul 17, 2020 · 2 comments · Fixed by #1908
Closed

Tutorial "Loading ImageJ ROI Sets" #1899

giovp opened this issue Jul 17, 2020 · 2 comments · Fixed by #1908
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@giovp
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giovp commented Jul 17, 2020

Is your feature request related to a problem? Please describe.
In the tutorial Loading ImageJ ROI Sets it's unclear how to get/generate the ROI.zip file.

The explanation for ImageJ seems quite clear, but it's not clear what image to use for that specific task. I also looked for the image in ~/.starfish/cache but could not find any pointer to the MERFISH data (which I assume is the one needed for the tutorial). This is also related to the assigning spot to cells tutorial

Describe the solution you'd like
either include ROI in starfish.data or better explanation how to generate the files.

Describe alternatives you've considered

Additional context
This issue references the JOSS submission openjournals/joss-reviews#2440

@neuromusic
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Thanks for calling this out, @giovp !!

We want to explicitly demonstrate loading from a file, so here's the plan:

  • Update the example to download RoiSet.zip from the blob on Github
  • load from the downloaded file

@mattcai
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mattcai commented Jul 29, 2020

In order to preserve the ability for readthedocs to render example gallery in the future (#1865), we chose to comment out the code that downloads RoiSet.zip from github.

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