Define BigDataViewer dataset xml to join several planes

bigdataviewer
bigstitcher
Tags: #<Tag:0x00007fa3075003c8> #<Tag:0x00007fa307500260>

#1

Dear BigDataViewer / BigStitcher community,

EDIT: I think I found the answer to my problem in another post: The BigStitcher does currently not support z-plane saved as single files. Ill try to concatenate the planes into a stack in Fiji to move on.

We have data from a 2P microtome which creates both physical sections as well as optical sections and can be used to image an entire organ.

Per physical section, my data has the dimensions 3 CH, 3 optical sections, 150 tiles per optical section and channel, 1 time point, saved as individual tif images in a single folder.

I have uploaded the first two physical sections of this dataset for reference, please feel free to have a look ( ~70 MB).

Using the Automatic loader I have succeeded in defining one xml per optical section, i.e. three h5/xml per folder.

I would now like to join all optical sections across all physical sections to define one large h5/xml that contains the entire dataset. Is this possible?

The naming convention is as follows:

  • folders containing a physical section are consecutively named, eg myplane-0001, myplane-0002 etc.
  • the tif files inside the folder are named date-time-tile{absolute number in entire volume}_channel{1-3}.tif
  • here the first 150 x 3 images comprise the optical section 1, the next 150 x 3 images make up optical section two and the remaining 150 x 3 images are optical section 3.

Thank you for your help and cheers,
Kai