search

catalystneuro / tye-lab-to-nwb

NWB Conversion project for the Tye lab at the Salk Institute.
MIT License
0 stars 0 forks source link

Add confocal images #15

Closed weiglszonja closed 1 year ago

weiglszonja commented 1 year ago

The histology data is in Olympus Image File format which includes a main setting file (.oif) and an associated directory with data and setting files (.tif, .bmp, .txt, .pty, .roi, and .lut).

I'm using the oiffile package to load the image and metadata to write the images to NWB. Currently I'm using the name and version of the software (e.g. FLUOVIEW FV1000, 1.2.6.0) and the depth information. Currently I'm creating an Images container and adding a GrayscaleImage per file (24 files in total) with a name and description using the extracted metadata.

@CodyCBakerPhD I'm not sure if there is an extension for storing all relevant metadata that can be extracted from the setting files, if not, in the future it might be worth creating one.

CodyCBakerPhD commented 1 year ago

I'm not sure if there is an extension for storing all relevant metadata that can be extracted from the setting files, if not, in the future it might be worth creating one.

I'm not familiar with any, but yeah eventually would be a great thing to have!

CodyCBakerPhD commented 1 year ago

The example file seems to have only the images per 6-depth

So for the final aggregated .oif file, that's not being written yet?

weiglszonja commented 1 year ago

So for the final aggregated .oif file, that's not being written yet?

The final aggregated images are in .tif format, I just extended the interface to write those images as well. The data in sub-H28_ses-1+image.nwb should include that now.