Commit 6a204764 authored by Christoph Sommer's avatar Christoph Sommer
Browse files

update doc 2

parent fa085838
## seg2dendrite
<img src="assets/dendrite+spines_5_1200x400.jpg" alt="Morse and Watson (Jonas group, unpublished)" style="width:600px;"/>
<img src="assets/dendrite+spines_5_1200x400.jpg" alt="Morse and Watson (Jonas group, unpublished)" style="width:512px;"/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Morse and Watson (Jonas group, unpublished)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.
......@@ -13,6 +14,7 @@ Choose a folder with images and a filetype (e. g. .ims). If your data is stored
multi-resolution, choose a resolution level (1: original resolution; 2 (default): down scaling by factor of 2).
### 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
......@@ -20,6 +22,7 @@ Note, if the Pixel Classification workflow is not working with your data, try
the `Autocontext` workflow.
### 3. Convert probability maps to dendrite objects and save as .swc for import in Imaris
---
#### Command line tool:
Extract the dentritic spine skeletons graph from ilastik probability maps and export to .swc for import in Imaris
......@@ -50,6 +53,8 @@ optional arguments:
See Jupyter notebook file
### 4. Import results to Imaris
---
####
Install the [.swc importer](./imaris_swc_impex) as a Imaris Python extension.
......@@ -57,7 +62,7 @@ Install the [.swc importer](./imaris_swc_impex) as a Imaris Python extension.
After pixel classification with ilastik on resolution level 2, which created a probability map volume_Probabilities.h5, use
```
python ilastik2dendrite.py volume_Probabilities.h5 --smooth 0.5 1 1 --threshold 0.5 -min_sizes 12000 --resolution_level 2
python seg2dendrite.py volume_Probabilities.h5 --smooth 0.5 1 1 --threshold 0.5 -min_sizes 12000 --resolution_level 2
```
it will smooth the probability map with sigma ZYX of 0.5 x 1 x 1 and threshold at probability 0.5, filter dendrite objects for minimum size of 12000px.
......
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