This page explains a way to use ilastik classification from FIJI/ImageJ, using the BIOP wrapper.
You cannot do the training within FIJI, this needs to be done in ilastik. However, once you have an ilp file, you'll be able to use it to perform ilastik classification from within FIJI/InageJ.
A practical example is given here (link TODO)
= Setting up the FIJI Ilastik Bridge ( needs to be done once ) =
== Install ilastik on your computer ==
https://www.ilastik.org/
== Enable BIOP fiji udate **dev** site: ==
BIOP-Dev Update site (https://biop.epfl.ch/Fiji-Update-Dev/)
== Make the connection between ilastik and Fiji ==
Fiji needs to know where the main ilastik executable file is located.
This needs to be done once. After FIJI will remember it (as long as you do not remove or change ilastik location on your HDD)
* In FIJI : click `Plugins > BIOP > Ilastik > Set Ilastik Location`
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* Click Browse in front of `IlastikExecutable` (take care : do not choose Elastix, it's something different! ) and select the location of the ilastik exe file.
** Typically on windows: `C:\Program Files\ilastik-[version]\ilastik.exe`
** TODO : find typical ilastik location in Mac
* Press OK and then click `Window > Console`.
You should see:
```
[INFO] Ilastik was found ;-)
```
= Ilastik side : make your classifier and set appropriate export settings =
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= Practical example =
= More information =
== What's supported ==
What is supported by the bridge:
* Image type supported:
** Single fluorescence channel
** RGB Images
* Ilastik taks:
** Pixel classification
** Multicut
* Export:
** Label image
** Probability map
What's known as currently unsupported:
* Image type supported:
** Multi fluorescence images
** Time Series ( to check )
* Ilastik taks:
** Object classification only