Scale_factors.json for starfish format MERFISH data example

I was attempting to work through the format_merfish_U2OS_data.py file given by the Format MERFISH data example in the documentation. I downloaded the data from the S3 bucket and tried to run the file, but it says I’m missing a scale_factors.json file. It was not in the files downloaded from the S3 bucket so I don’t know where this is supposed to come from. I’m new to MERFISH and imaging transcriptomics in general so I’m not sure what I’m missing.

Seems you are right, the scale_factors.json is missing from the data. Sorry about that. However, if you are just trying to work through a data formatting example then you can skip the scale_factors (just remove postprocess_func=add_scale_factors,). The scale_factors were originally provided for precise image normalization that matched the author’s (see: pixel-based decoding tutorial). This is not a requirement of most image-based transcriptomics, but it shows the flexibility of the SpaceTx format to store and use extra information.

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