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.
points_to_brainrenderis 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.
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.
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
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