starfish
starfish copied to clipboard
spacetx
starfish: unified pipelines for image-based transcriptomics
Spot decoding strategies based only on intensity look-up of the max-valued channel in each sequencing round can be prone to false decoding when fluorescent spots are highly clustered together or...
An user should leverage parallelism on HPC clusters to run starfish and process volumetric data like seqFISH data (s3://spacetx.starfish.data.public/seqfish/). I am wondering if it is possible roughly estimate CPU/GPU numbers...
@christoffermattssonlangseth @xyanqian noted that starfish restricts global coordinate space to micrometers, but that it could be helpful to operate on the global space in pixels, as well. Would others find...
#### Description #1808 erroneously removed the code that detected whether we are working with 2d or 3d data. however, it is possible to call trackpy spot detection with `is_volume=False` and...
https://github.com/spacetx/starfish/blob/47de54081c61e68932364a7fb53ed0f6cb5752b5/starfish/core/spots/FindSpots/trackpy_local_max_peak_finder.py#L134
https://github.com/spacetx/starfish/blob/0106f031edc641ae0fef595548d9b1030679d591/starfish/core/imagestack/imagestack.py#L1057
https://github.com/spacetx/starfish/blob/ad9010fa7533052efaebee051a48d15cf28e2266/starfish/core/types/_spot_attributes.py#L47
https://github.com/spacetx/starfish/blob/339eaa9bb67744cadc04379f18a953653929a555/starfish/core/morphology/Binarize/threshold.py#L42
https://github.com/spacetx/starfish/blob/6c3bf46da08628e6c9c44891eb3d315eb21581bc/starfish/core/codebook/codebook.py#L686
https://github.com/spacetx/starfish/blob/ff43229f46e1eaed87d5c978ea8db6c5b2ced6f7/starfish/core/_display.py#L260