ShuTu: needs a data index file to read Allen image stacks

reconstrue / brightfield

Reconstruction of biocytin-stained neurons detected in brightfield microscopy image stacks

http://reconstrue.com

Apache License 2.0

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Open JohnTigue opened 5 years ago

JohnTigue commented 5 years ago

See the ShuTu tutorial for multiple examples of datsets being loaded. Datasets generated multiple ways.

JohnTigue commented 5 years ago

Main example, Granule Cell 63X Start uses an XML file generated by Zeiss ZEN.

JohnTigue commented 5 years ago

fly motor neurons has .tif files that contain multiple images in one file. These seem to be called multi-page TIFFs, or in PIL's words "Multi-frame TIFF Images."

That's not how the challenge data is presented. So, this will not work:

ShuTuAutoTraceOneStack some_multi_frame.tif some_shutu_config.dat

JohnTigue commented 5 years ago

I think the .tif files in the challenge are pre-stitched so don't even need to do first step?

JohnTigue commented 5 years ago

The main ShuTu distro comes with various *.dat files:

These do not contain any info about the image stack, so something else is providing the index to the image stack.

JohnTigue commented 4 years ago