search

JaneliaSciComp / multifish

EASI-FISH analysis pipeline for spatial transcriptomics
BSD 3-Clause "New" or "Revised" License
32 stars 13 forks source link

Add RS-FISH parameters for multiple channels #20

Open neugun opened 1 year ago

neugun commented 1 year ago

Hi Konrad and Cristian,

I am wondering if I can use different RS-FISH parameters for spot extraction or can you please add this feature? Please see the following request.

New feature

RS-FISH parameters for multiple channels

Proposal

Any possible way to use different RS-FISH parameters for multiple channels?

Usage scenario

Spot extraction

Thanks a lot! Best Zhenggang

cgoina commented 1 year ago

Could you be a bit more specific - what parameters would you like to have. If you use airlocalize for spot extraction we are somewhat limited by the parameters supported by airlocalize and unfortunately we are not in control of that tool. If you use the spark version for spot extraction we may have a bit more flexibility since that is a tool developed at Janelia.

neugun commented 1 year ago

Thank you so much, Cristian! Yes, the parameters for RS-FISH (spark version for spot extraction) will be "rsfish_anisotropy","rsfish_sigma",and "rsfish_threshold". Now, these 3 parameters are used for all channels but I am wondering if we can assign these 3 parameters differently for each image channel. Thanks!

cgoina commented 9 months ago

These have been added and documented in the Parameters.doc and also added to the nextflow_schema. In the schema they appear like: "per_channel.rsfish_min" or "per_channel.rsfish_min" and the take a comma delimited list of values. The list must be the same length as the number of channels, e.g. if channels are c0,c1,c2 then per_channels.rsfish_min should be "c1val, c2val,c3val"