Visium dbs with multiple subfolders/types in the ./spatial subfolder

[Farbodch]

Two of the visium readers' inputs are fullres_image_file and scalefactors_file.
Some of the visium dbs (below) have multiple subfolders/types in their ./spatial subfolder, each with their own distinct image_ & scalefactors_ files. It is unclear how these should be parsed into the visium reader, which expects only one file for each of the two inputs.

The visium dbs in question:

• data/gulca__10X__Visium__Mouse__brain__20220311__v1.3.1 db on 10x website
• data/h3jfi__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AggregateofTissueCores db on 10x website
• data/uloap__10X__Visium__Mouse__brain__20220714__v2.0.0 db on 10x website
• data/zwowd__10X__Visium__Mouse__brain__20220714__v2.0.0 db on 10x website

with

• 12 subfolders in gulca_
• 9 subfolders in h3jfi_
• 2 subfolders in uloap_
• 2 subfolders in zwowd_

in ./spatial/*

note also: the above dbs are the only "proper" visium dbs without a tissue_positions_file file.
("proper" as opposed to the two dbs 3554v_ & 0nuqa_ that are missing the major .h5 file. Refer to another issue for these two)

[Farbodch]

The following db doesn't have their sub-sections individually and separately downloaded:

• gulca__10X__Visium__Mouse__brain__20220311__v1.3.1 link to db on 10x website

#28

[Farbodch]

The x2 subsections of the following aggregated DB already exists:

• uloap__10X__Visium__Mouse__brain__20220714__v2.0.0 db on 10x website

They are the following:

• 3s126__10X__Visium__Mouse__brain__20220713__v2.0.0 Mouse Brain Coronal Section 1 (FFPE)
• p1yrb__10X__Visium__Mouse__brain__20220713__v2.0.0 Mouse Brain Coronal Section 2 (FFPE)

#25

[Farbodch]

The x2 subsections of the following aggregated DB already exists:

• zwowd__10X__Visium__Mouse__brain__20220714__v2.0.0 db on 10x website

They are the following:

• d3ykk__10X__Visium__Mouse__brain__20220712__v2.0.0 Mouse Brain Serial Section 2 (Sagittal-Anterior)

  • Suspected Duplicate: sj4fv__10X__Visium__Mouse__brain__20220712__v2.0.0
  • Suspected Duplicate: zztm8__10X__Visium__Mouse__brain__20220712__v2.0.0

• xtaqh__10X__Visium__Mouse__brain__20220712__v2.0.0 Mouse Brain Serial Section 2 (Sagittal-Posterior)

• Suspected Duplicate: zfcqw__10X__Visium__Mouse__brain__20220712__v2.0.0

• Suspected Duplicate: zwdai__10X__Visium__Mouse__brain__20220712__v2.0.0

#26

[Farbodch]

The x11 subsections of the following aggregated DB already exists:

• h3jfi__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AggregateofTissueCores db on 10x website

They are the following:

• jezks__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__InputsLibrary
• vrwlc__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__AllTissueCores
• uk0rv__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate1
• 0ufac__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate2
• bw2x9__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate3
• f0fww__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__BrainReplicate4
• th4zp__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate1
• 5nwfc__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate2
• vt6x9__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate3
• 4b368__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate4
• 9btjk__10X__Visium__Mouse__lung_brain__20230221__v2.0.1__LungReplicate5

#27