XitoSBML is an ImageJ plugin which creates a Spatial SBML model from segmented images. XitoSBML is not just a converter, but also a spatial model editor so that users can add molecules(species), reactions, and advection/diffusion coefficients to the converted Spatial SBML model.
- Launch ImageJ (Fiji)
- Click [Help] -> [Update...]
- Click [Manage update sites] button on [ImageJ Updater] dialog
- On [Manage update sites dialog], scroll down the list of update sites, turn on [XitoSBML] checkbox and press [Close] button
- Click [Apply changes] button on [ImageJ Updater] dialog
- ImageJ (Fiji) will download and install XitoSBML and its dependent libraries
- Restart ImageJ (Fiji); then you will find [XitoSBML] plugin under [Plugins] menu
Here is a screencast of the above installation procedure (screencast is also available as an MP4 file).
XitoSBML requires segmented images to create spatial model. Please prepare segmented images of original microscopic images beforehand. The segmented images will be obtained by using pre-built Segmentaion function in ImageJ.
- Launch ImageJ (Fiji)
- Load original images (not mandatory) and their segmented images
- Click [Plugins] -> [XitoSBML] -> [run Spatial Image SBML Plugin]
- On [DomainType Namer] dialog, assign an opened segmented image to each organelle (ex. nucleus, cytosol)
- XitoSBML will ask whether you want to add SBML objects (Species, Reactions, and Parameters) to the converted Spatial SBML model. If you just want to convert your segmented image files to Spatial SBML, then just click [No]
- Specify a filename of converted SBML model
- XitoSBML will display the converted Spatial SBML document and Domain Hierarchy of your model to let you confirm the converted result
- Exported SBML and the merged segmented image will be stored (where you specified in step 6)
Here is a screencast of the above procedure (screencast is also available as an MP4 file).
This repository also contains example 2D and 3D images and converted Spatial SBML models under examples directory. Here is a description on example files.
directory | filename | input or output | description |
---|---|---|---|
examples/2D |
Rat_Hippocampal_Neuron-Nuc.tiff |
input | 2D segmented image of nucleus |
examples/2D |
Rat_Hippocampal_Neuron-Cyt.tiff |
input | 2D segmented image of cytosol |
examples/2D |
example2D.xml |
output | 2D spatial SBML model generated by XitoSBML |
examples/2D |
example2D.tiff |
output | 2D merged segmented image generated by XitoSBML |
examples/2D |
Rat_Hippocampal_Neuron-Hoechst.tiff |
-- | Original 2D fluroscent microscopic image of nucleus |
examples/2D |
Rat_Hippocampal_Neuron-NicotinicAcetylcholineAlpha7.tiff |
-- | Original 2D fluroscent microscopic image of cytosol |
directory | filename | input or output | description |
---|---|---|---|
examples/3D |
nuc-zstack.tiff |
input | 3D (Z-stack) segmented image of nucleus |
examples/3D |
cyt-zstack.tiff |
input | 3D (Z-stack) segmented image of cytosol |
examples/3D |
zstack.xml |
output | 3D spatial SBML model generated by XitoSBML |
examples/3D |
zstack.tiff |
output | 3D (Z-stack) merged segmented image generated by XitoSBML |
Next example will show how to create a Spatial SBML model, add SBML objects to the model, and make it as a mathematical model. The following figure represents the diagram of this example model. Note that species A
and B
diffuse inside the nucleus and cytosol with the given diffusion coefficients (Dnuc
and Dcyt
), respectively.
- Launch ImageJ (Fiji)
- Load original images (not mandatory) and their segmented images
- Click [Plugins] -> [XitoSBML] -> [run Spatial Image SBML Plugin]
- On [DomainType Namer] dialog, assign an opened segmented image to each organelle (ex. nucleus, cytosol)
- XitoSBML will ask whether you want to add SBML objects (Species, Reactions, and Parameters) to the converted Spatial SBML model. This time, we want to add SBML objects so click [Yes]
- In [Species] tab, add species
A
andB
. Note that we will add speciesA
to Nucleus andB
to Cytosol - In [Diffusion] tab, add
Diffusion coefficient
for speciesA (Dnuc)
andB (Dcyt)
- In [Reaction] tab, add a reaction (
A -> B
) and its kinetic law. Please do not forget to assign reactants and products for the reaction - Specify a filename of converted SBML model
- XitoSBML will display the converted Spatial SBML document and Domain Hierarchy of your model to let you confirm the converted result
- Exported SBML and the merged segmented image will be stored (where you specified in step 9)
Here is a screencast of the above procedure (screencast is also available as an MP4 file).
You can find example 2D and 3D images and converted Spatial SBML model under examples directory.
The mathematical (spatial) model created by this example can be executed by several spatial simulators which support Spatial SBML. For example, you can use our SpatialSimulator for executing the converted model. We have provided a Docker image for SpatialSimulator so that you can easily install and run SpatialSimulator on your environment.
git clone https://github.com/funasoul/docker-spatialsim.git
cd ./docker-spatialsim/
# Copy example2D.xml to this directory
./docker-spatialsim.sh -t 0.2 -d 0.0001 -o 50 example2D.xml
SpatialSimulator will generate numbers and images of the simulation result.
Species A | Species B |
---|---|
To whom might be interested, here is an instruction on how to compile XitoSBML from source code.
XitoSBML requires the following third-party applications/libraries.
- JSBML
- Fiji Is Just ImageJ
- ImageJ 3D Viewer version 1.5 or higher
- Maven
% git clone https://github.com/spatialsimulator/XitoSBML.git
% mvn install -Dimagej.app.directory=/path/to/ImageJ
For example, if you want to build XitoSBML on Fiji.app(MacOSX), the mvn
command will be executed as follows:
% mvn install -Dimagej.app.directory=/Applications/Fiji.app/
Javadocs of XitoSBML API are included under apidocs
directory in the repository, and
are available on our web site.
Here are the high-level key classes of XitoSBML, which will be a good starting point to read through the code.
Class | Plugin item on ImageJ |
---|---|
jp.ac.keio.bio.fun.xitosbml.xitosbml.MainImgSpatial.java | run Spatial Image SBML Plugin |
jp.ac.keio.bio.fun.xitosbml.xitosbml.MainModelEdit.java | run Model Editor |
jp.ac.keio.bio.fun.xitosbml.xitosbml.MainModelValidator.java | run Model Validation |
XitoSBML is licensed under the Apache License, Version 2.0. See LICENSE for the full license text.