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janfpl
@janfpl
Hello! I recently found out about the cellfinder package and I am very excited to try it. Is there a tutorial dataset available?
Adam Tyson
@adamltyson
There will be soon. Is there anything in particular you want to do?
janfpl
@janfpl
For now, I only have slides with serial coronal sections of mouse brain spaced 300um apart. Is it possible to register single sections? I will have light sheet data in a few weeks and I just wanted to get familiar with the package so that I'm ready to analyze my whole brain data when I have it.
Adam Tyson
@adamltyson
Currently it’s only for 3D data, but we’re looking to add 2D support. If you have data you can share, that would be great.
Jun
@Jun-Lizst
Hello! everyone, I just find out cellfinder will be useful. trying recently.
vatsal mehra
@rdbcasillas
@adamltyson Is this the right room to ask questions about cellfinder's code?
Adam Tyson
@adamltyson
Yeah anywhere is fine really, but there's also cell detection if your query is specifically about that or dev if its about contributing to cellfinder.
vatsal mehra
@rdbcasillas

cool, thanks @adamltyson. I will just ask here since it doesn't seem directly relevant to other channels.

im looking into points_to_brainrender script and trying to modify it based on our data. I notice that you assign "max_z" as 13200 and then subtract the value of cell[x] from that to get new cell[x] values. Is this because you wanted to flip the x values as your data is coronal images? How did you come up with "max_z"? After changing few things, we have realized we want to flip cell["y"] values but not sure how to find out "max_y" to subtract those values from.

We also had to change line 35 from [z,y,x] to [z,x,y] which probably helps with our sagittal images.

Adam Tyson
@adamltyson
Hey, sorry that points_to_brainrender is in such a mess. I might have mentioned, but the reason is I will soon be moving cellfinder from using amap to brainreg, which will deal with orientation & scaling issues in a much better way.
The 13200 comes from the allen atlas reference volume which is 13200 x 8000 x 11400 microns. max_z is the the length of the allen reference volume (which brainrender's coordinate space). If you want max y, it will be 8000 or 11400 depending on your data's orientation.
All of this stuff will be fixed in the next cellfinder release.
Out of interest, if you're at the stage of visualising detected cells in brainrender, I'd love to see what you're doing with cellfinder. I usually only get to see when it goes wrong for people!
vatsal mehra
@rdbcasillas

thanks a lot, this seems useful.

scientists I am working with are labeling the neurons in mouse brains that connect to the spinal cord and they brought me in (a bioinformatics guy) to use some of these tools (including cellfinder and brainrender) to identify exact location of cells that they have labelled.

they do have a paper they are working on so of course we will be citing cellfinder. What kind of info you are looking to see?
1 reply
sthitapati
@sthitapati

Hi Adam! I am running the updated version of cellfinder with the command:

cellfinder -s "/home/sthitapati/Desktop/D1CreRabies/stitchedImages_100/2" -b "/home/sthitapati/Desktop/D1CreRabies/stitchedImages_100/3" -o "/home/sthitapati/Desktop/D1CreRabies/output" -v 5.0 2.231 2.231 --orientation psl.

I am getting the following error. Traceback (most recent call last):
File "/home/sthitapati/anaconda3/envs/cellfinder/lib/python3.7/concurrent/futures/process.py", line 239, in _process_worker
r = call_item.fn(call_item.args, *call_item.kwargs)
File "/home/sthitapati/anaconda3/envs/cellfinder/lib/python3.7/site-packages/imio/load.py", line 457, in load_from_paths_sequence
anti_aliasing=anti_aliasing,
File "/home/sthitapati/anaconda3/envs/cellfinder/lib/python3.7/site-packages/skimage/transform/_warps.py", line 265, in rescale
raise ValueError("Supply a single scale, or one value per spatial "
ValueError: Supply a single scale, or one value per spatial axis
"""

4 replies
sthitapati
@sthitapati