Change Details

This page will allow you to use ilastik classification from FIJI/ImageJ. 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. = 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 > Set And Check Wrappers` {F13329821, width=100%} * 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 * You do not need to fill the rest of the executable file locations ( this will create some errors, but that's ok ). * Press OK and then click `Window > Console`. You should see: ``` [INFO] Elastix -> not set :-( Ilastik -> set :-) Transformix -> not set :-( ``` What's important is the line concerning ilastik, you should get a `set :-)`

This page will allow you to use ilastik classification from FIJI/ImageJ. 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. TODO : INSERT Outline 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 = 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 > Set And Check Wrappers` {F13329821, width=100%} * 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 * You do not need to fill the rest of the executable file locations ( this will create some errors, but that's ok ). * Press OK and then click `Window > Console`. You should see: ``` [INFO] Elastix -> not set :-( Ilastik -> set :-) Transformix -> not set :-( ``` What's important is the line concerning ilastik, you should get a `set :-)` = Ilastik side : make your classifier and set appropriate export settings =

This page will allow you to use ilastik classification from FIJI/ImageJ. 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. TODO : INSERT Outline 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 = 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 > Set And Check Wrappers` {F13329821, width=100%} * 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 * You do not need to fill the rest of the executable file locations ( this will create some errors, but that's ok ). * Press OK and then click `Window > Console`. You should see: ``` [INFO] Elastix -> not set :-( Ilastik -> set :-) Transformix -> not set :-( ``` What's important is the line concerning ilastik, you should get a `set :-)` = Ilastik side : make your classifier and set appropriate export settings =