Create singularity container to run Bruker Prairie View software

[chrisroat]

@vsoch, croat-singularity branch has the Dockerfile + instructions I've gotten written so far. The process worked once, but it turns out it was likely due to my external ~/.wine directory being mounted. Things stopped working when I ran the container after my ~/.wine directory was reset. The leads me to believe that I need to avoid mounting my home directory, and setup an container-internal ~/.wine directory -- but I don't know what is needed.

Dockerfile: https://github.com/deisseroth-lab/two-photon/blob/croat-singularity/Dockerfile

README with instructions https://github.com/deisseroth-lab/two-photon/blob/croat-singularity/README.md

This has been heavily influenced by dissecting a repo by @scotthardy, and it's docker-wine scripts https://github.com/scottyhardy/docker-wine https://github.com/scottyhardy/docker-wine/blob/master/docker-wine

[vsoch]

okay, I have the .exe that I found running in the Singularity container -

Do you have some dummy data I can test for the python script?

[tbenst]

@vsoch great to have your help on this!

Here's a sample data folder: https://drive.google.com/drive/folders/12niUpCXgOSX3sXFEdT-KhYjXCWVdhrE6?usp=sharing

The expected output is a single .tiff file like so: https://drive.google.com/file/d/1Vot4tO8BWdCDitALSexkibSO2sjPvHI-/view?usp=sharing (note that folder was named overview-23 on my computer rather than bruker-example, hence filename)

Indeed, we believe the raw data is 203MB while the tif of same data is 526kB, (proprietary data formats :man_shrugging:)

[vsoch]

Thank you! I'll give that a shot.

[tbenst]

if you get an error on conversion, you likely need to do winetricks -q vcrun2015

[vsoch]

Ha! Yes I did get that error, and realized I needed to install it.

[vsoch]

Sorry to be dense - stupid question - why is the image entirely black?

[vsoch]

Seems to be the right size!

$ ls -l overview-23/overview-023_Cycle00001_Ch3_000001.ome.tif 
-rw-r--r-- 1 vanessa vanessa 526404 Aug 30 13:32 overview-23/overview-023_Cycle00001_Ch3_000001.ome.tif

I'll open up a PR with instructions to reproduce this!

[vsoch]

It's so weird that the file lists and other supporting files just go away after you run it. I guess I'll chock this up to weird Windows logic :P

[tbenst]

Sorry to be dense - stupid question - why is the image entirely black?

Not dumb at all! It's just very dim. If you open with ImageJ/Fiji, you will see a very crummy picture of a zebrafish brain, symmetrical on x-axis...sorry I didn't choose a better photo ;)