Example dataset for CellMap and TubeMap about clearmap2

[ChristophKirst]

Hi, thanks for pointing this out, we are working on a smaller sample data set, Meanwhile, we have larger data sets uploaded:
CellMap:
https://osf.io/cztq2/
TubeMap:
https://osf.io/sa3x8/

Please let me know if this helps ?

[KHBHH]

Hi, is there a dataset that matches the tutorial dataset? https://www.youtube.com/watch?v=-WehURPyIa8

[KHBHH]

Also, is there a small data set version uploaded yet?

[ovalerio]

Hi Christoph,

I am also interested on getting the train dataset used in the ClearMap2 YouTube tutorial linked above.

I am aware of the CellMap article data in OSF https://osf.io/5qzn7/ at the idisco website.
In that link there is data in https://osf.io/rp2ev/ under the project name "Haloperidol injection".

I used the osfclient python library to clone the data locally.

 $ ls osfstorage/Haloperidol\ injection/Saline/
saline.7z.001  saline.7z.008  saline.7z.014  saline.7z.020  saline.7z.026  saline.7z.032  saline.7z.038  saline.7z.045  saline.7z.051  saline.7z.057  saline.7z.063  saline.7z.069
.... omitted output ...
saline.7z.007  saline.7z.013  saline.7z.019  saline.7z.025  saline.7z.031  saline.7z.037  saline.7z.044  saline.7z.050  saline.7z.056  saline.7z.062  saline.7z.068  saline.7z.074
 $ ls osfstorage/Haloperidol\ injection/Haloperidol/
haloperidol.7z.001  haloperidol.7z.011  haloperidol.7z.020  haloperidol.7z.029  haloperidol.7z.038  haloperidol.7z.048  haloperidol.7z.057  haloperidol.7z.066  haloperidol.7z.075
.. / omitted output ...
haloperidol.7z.010  haloperidol.7z.019  haloperidol.7z.028  haloperidol.7z.037  haloperidol.7z.047  haloperidol.7z.056  haloperidol.7z.065  haloperidol.7z.074

When I tried to uncompress those files I got an error:

 $ file osfstorage/Haloperidol\ injection/Saline/saline.7z.001
osfstorage/Haloperidol injection/Saline/saline.7z.001: 7-zip archive data, version 0.3

 $ 7za x osfstorage/Haloperidol\ injection/Saline/saline.7z.001 

7-Zip (a) [64] 16.02 : Copyright (c) 1999-2016 Igor Pavlov : 2016-05-21
p7zip Version 16.02 (locale=en_US.UTF-8,Utf16=on,HugeFiles=on,64 bits,80 CPUs Intel(R) Xeon(R) Gold 6230 CPU @ 2.10GHz (50657),ASM,AES-NI)

Scanning the drive for archives:
1 file, 699400192 bytes (667 MiB)

Extracting archive: osfstorage/Haloperidol injection/Saline/saline.7z.001
ERROR: osfstorage/Haloperidol injection/Saline/saline.7z.001
saline.7z
Open ERROR: Can not open the file as [7z] archive

ERRORS:
Unexpected end of archive

[ovalerio]

Hi Christoph,

I downloaded the big dataset that you shared in OSF. Now I'm trying to follow the CellMap.ipynb example.

I change the file names using the TagExpressions syntax.

I'm not sure if I got it right though, since I get an error about dimensions mismatch.

directory = '/scratch/cmap_data/190214-4R'    

expression_raw      = 'cFos/13-01-56_FOS_UltraII[<X,2> x <Y,2>]_C00.ome.tif'           
expression_auto     = 'Autofluorescence/14-48-51_auto_UltraII_C00_xyz-Table Z<Z,4>.ome.tif'  

ws = wsp.Workspace('CellMap', directory=directory);
ws.update(raw=expression_raw, autofluorescence=expression_auto)
ws.debug = True

resources_directory = settings.resources_path

This was the error I got when I want to visualize the data:

p3d.plot(ws.filename('raw'))

RuntimeError: Source has 5 > 4 dimensions: FileList-Source(1004, 1007, 1030, 8, 5)[uint16]<40>{/scratch/cmap_data/190214...os/13-01-56_FOS_UltraII[<X,2> x <Y,2>]_C00.ome.tif}!

Can you help?

Thanks!