Commit 23a2f63b authored by Christoph Sommer's avatar Christoph Sommer
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Add README.md

parent 83265627
### seg2dendrite
Trace dendrite and spine from ilastik segmentation and output .swc file for import into Imaris
#### Usage
```bash
usage: seg2dendrite.py [-h] [-ms MIN_SIZE] [-s SCALE]
ilastik_seg_h5 [ilastik_seg_h5 ...]
Extract skeletons from ilastik dendtite segmentation and export to .swc for
import in Imaris
positional arguments:
ilastik_seg_h5
optional arguments:
-h, --help show this help message and exit
-ms MIN_SIZE, --min_size MIN_SIZE
-s SCALE, --scale SCALE
```
#### Reuires
Python 3.x
* h5py
* skan
* numpy
* networkx
* skimage
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