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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 a properly set ilastik project file (with ilp extension), you'll be able to perform ilastik classification from within FIJI/InageJ, in a convenient and easily scriptable/recordable manner. A practical example is given here (link TODO) = Setting up the FIJI Ilastik Bridge ( needs to be done once ) = == Install ilastik on your computer == Installer can be find on https://www.ilastik.org/ == Enable BIOP fiji udate **dev** site: == In FIJI, click Help > Update > Add Update Site. In the new line created: * put any name you like in the column Name (like BIOP-DEV) * put `https://biop.epfl.ch/Fiji-Update-Dev/` in the URL column * click Close then Apply changes, then restart FIJI == 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` {F13336242, 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 * Press OK and then click `Window > Console`. You should see: ``` [INFO] Ilastik was found ;-) ``` = Ilastik side : make your classifier and set appropriate export settings = {F13330086, width=100%} = 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

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 a properly set ilastik project file (with ilp extension), you'll be able to perform ilastik classification from within FIJI/InageJ, in a convenient and easily scriptable/recordable manner. A practical example is given here (link TODO) = 1 - Setting up the FIJI Ilastik Bridge ( needs to be done once ) = == 1.a. Install ilastik on your computer == Installer can be find on https://www.ilastik.org/ == 1.b. Enable BIOP fiji udate **dev** site: == In FIJI, click Help > Update > Add Update Site. In the new line created: * put any name you like in the column Name (like BIOP-DEV) * put `https://biop.epfl.ch/Fiji-Update-Dev/` in the URL column * click Close then Apply changes, then restart FIJI == 1.c. 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` {F13336242, 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 * Press OK and then click `Window > Console`. You should see: ``` [INFO] Ilastik was found ;-) ``` = 2 - Practical example : cell / nuclei pixel classification = == 2.a. Make a pixel classifier with ilastik == Use ilastik as usual, but set (WARNING) blabla {F13330086, width=100%} = 3 - More information = == What's currently supported in the ilastik fiji bridge == 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 == Troubleshooting ==

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 a properly set ilastik project file (with ilp extension), you'll be able to perform ilastik classification from within FIJI/InageJ, in a convenient and easily scriptable/recordable manner. A practical example is given here (link TODO) = 1 - Setting up the FIJI Ilastik Bridge ( needs to be done once ) = == 1.a. Install ilastik on your computer == Installer can be find on https://www.ilastik.org/ == 1.b. Enable BIOP fiji udate **dev** site: == In FIJI, click Help > Update > Add Update Site. In the new line created: * put any name you like in the column Name (like BIOP-DEV) * put `https://biop.epfl.ch/Fiji-Update-Dev/` in the URL column * click Close then Apply changes, then restart FIJI == 1.c. 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` {F13336242, 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 * Press OK and then click `Window > Console`. You should see: ``` [INFO] Ilastik was found ;-) ``` = 2 - Practical example : cell / nuclei pixel classification = == 2.a. Make a pixel classifier with ilastik == = Ilastik side : make your classifier and set appropriate exporUse ilastik as usual, but settings = {F13330086, width=100%}t (WARNING) blabla = Practical example = {F13330086, width=100%} = 3 - More information = == What's currently supported ==ted in the ilastik fiji bridge == 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 == Troubleshooting ==