Commit 7c11f863 authored by Christoph Sommer's avatar Christoph Sommer
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update doc 2

parent 6a204764
## seg2dendrite
## Seg2dendrite:
#### Automatic 3D Dendritic Spine Quantification with ilastik and Imaris
---
<img src="assets/dendrite+spines_5_1200x400.jpg" alt="Morse and Watson (Jonas group, unpublished)" style="width:512px;"/>
Morse and Watson (Jonas group, unpublished)
### 1. Convert your images (.ims; or other) to .h5 for pixel classification in ilastik
---
Use the ImageJ macro `img2h5.ijm` to convert .ims files to ilastik .h5 files. Note,
that the `ilastik` update site needs to be enabled in Fiji.
......@@ -15,6 +17,7 @@ multi-resolution, choose a resolution level (1: original resolution; 2 (default)
### 2. Use ilastik pixel classificaiton
---
Use `Pixel Classification` workflow.
* Choose dendrite class as first class in training (yellow color)
* Make sure probability maps are exported as uint8 and renormalized to 0-255
......
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