In Situ Sequencing Segmentation
Use the package manager pip to install is3g:
pip install is3g
See example.ipynb Jupyter Notebook for a minimal example.
You can also use the is3g command to execute is3g from the command-line. For example:
$ is3g examples/data.csv examples/data_out.csv --x X --y Y --label Gene --radius 22.5
Training on device: cpu
Epoch 222: loss=0.461070, accuracy=0.784571:
44%|████████████████████████████ | 221/500 [00:06<00:08, 34.86it/s]
Stopping early at epoch 221 with loss 0.4128You can list all options with:
$ is3g --help
Usage: is3g [OPTIONS] CSV_PATH CSV_OUT
Options:
-x, --x TEXT Column in the CSV file where the x coordinate is stored for each gene.
-y, --y TEXT Column in the CSV file where the y coordinate is stored for each gene.
-l, --label TEXT Column in the CSV file where the gene labels are stored.
-r, --radius FLOAT RANGE Approximate radius of a cell. [x>=0]
--remove-background / --no-remove-background
Specify whether to automatically remove genes from low-density regions. Default is true.
--version Show the version and exit.
--help Show this message and exit.If (when) you find a bug, please raise an issue.
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.