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

[JohnTigue]

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

[JohnTigue]

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

[JohnTigue]

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]

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

[JohnTigue]

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

• ShuTu.Parameters.100X.dat
• ShuTu.Parameters.63X.dat
• ShuTu.Parameters.flyMotorNeuron.dat
• ShuTu.Parameters.granule63XTest.dat
• ShuTu.Parameters.Purkinje.dat

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

[JohnTigue]

https://pypi.org/project/tifffile/

tifffile and TIFWriter: Create a Z-stack with numpy