-
Notifications
You must be signed in to change notification settings - Fork 28
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Running 3D Segmentation #111
Comments
I am running into a similar issue, which I highlighted in a bit more detail in this other issue here. |
@FalkoHof Thanks so much for linking your issue. It seems like your run got to the point where 3D segmentation was at least recognized. Out of curiosity, what did you do differently to at least get to that point, even if your run ultimately errored out because of the too many z values issue? |
The 3D segmentation was working for me irrespectively of using floats or ints on the z-axis. However, the json was only outputing 2D data. What kind of data are you using as input? I used Xenium data and followed this workflow (but deviated a bit from it due to changes in baysor and the xenium output). The modifications I made to the workflow were mostly to the main method of the filter_transcripts.py. script. See below:
@NickDiNapoli What is the error baysor is throwing in your case? |
I am trying to obtain a 3D segmentation result from what I believe is the way to do so. I am not using
PRIOR_SEGMENTATION
in this run.z
column name in theMOLECULES_CSV
via'-z'
parameterforce_2d = false
in theconfig.toml
fileThe README documentation explains:
segmentation_polygons.json: polygons used for visualization in GeoJSON format. In the case of 3D segmentation, it is an array of GeoJSON polygons per z-plane, as well as "joint" polygons. Shown only if
--save-polygons=geojson
is set.The output GeoJSON only contains one set of 2D geometries instead of the expected output above. Can you please advise what aspect I am missing to obtain a 3D output?
Run parameters:
~/.julia/bin/baysor run
'transcripts.csv'
-c 'example_config_3d.toml'
-x 'global_x' -y 'global_y' -z 'global_z' -g 'gene' -m 20 -s 5
--save-polygons=geojson
-p
-o 'test'
Environment is:
NAME="Amazon Linux AMI"
VERSION="2018.03"
The text was updated successfully, but these errors were encountered: