YangLabHKUST / STitch3D

Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices

https://stitch3d-tutorial.readthedocs.io/en/latest/index.html#

MIT License

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Cannot find CCFv3 dataset #14

Closed cristalliao closed 1 year ago

cristalliao commented 1 year ago

Dear Professor, I want to know where I can find this file when I try this great STitch3D.

3D coordinates and model are based on CCFv3.

load("spotstable.RData") load("VOLUMESMALL.RData") load("VOLUME.RData") in this part, "Run STitch3D on the adult mouse brain dataset" Thank you so much!

gefeiwang commented 1 year ago

Hi Cristal,

"spotstable.RData" is a data frame named "spots.table", containing meta information of spots. You can get this data frame by including sources provided by the original publication following this code. Then run spots.table <- add.parent.acronym(load.spots.table()) to get the data frame.

"VOLUMESMALL.RData" and "VOLUME.RData" contain 3D mesh models of mouse brain. You can load them by running the following code: library(wholebrain) attach(loadNamespace('wholebrain'), warn.conflicts = FALSE) which depends on package "wholebrain".

cristalliao commented 1 year ago

Dear Gefei, Thanks for your reply! It is really helpful!! However, I still cannot run the sources provided by the original publication following this code, the R studio gives me the error:

Do you know how to deal with this problem? Thanks a lot!

gefeiwang commented 1 year ago

Hi Cristal,

You may need to also modify path.bin and path.matrices to the corresponding folders.