Simulation results generated by VCell can be very large, depending on the mesh and time resolution then can take several GBs. VCell Simulation Results Viewer Plugin enables the remote viewing and analysis of these data sets in ImageJ without the need to download data to your computer and import it to Fiji/ImageJ. It supports ImageJ compatible remote storage image format *.N5. New VCell features include:
- Spatial simulation results in VCell can be prepared for export in N5 formats but still stored on the remote server
- The link to simulation results enabled them to be opened by any imaging software supporting N5
- The ImageJ/Fiji VCell Simulation Results Viewer Plugin can import VCell simulation results directly into Fiji.
Install FIJI/ImageJ VCell Simulation Results Viewer Plugin
In FIJI:
Help -> Update… (Not Update ImageJ…) -> Manage Update Sites -> Add unlisted sites -> Paste https://sites.imagej.net/VCell-Simulations-Result-Viewer/ (ensure this new entry has a check mark next to it) -> Apply and Close -> Apply Changes -> Restart. You may need to close and open Fiji.
Prepare N5 export in the VCell.
To prepare simulation data to be used remotely, go to Simulation Results -> Export Data, and select ImageJ compatible remote storage (*.N5) as an Export Format. Currently, the N5 export only supports volume data variables. Select the variables to export with the required Export Time interval, then click Start Export. A pop-up for settings related only to N5 will appear asking for what compression type you want for the export, and the name this export will have. The export will generate the N5 data set on VCell remote server, and you can get the path to the dataset via Copy Link button.
View simulation results in Fiji/ImageJ on the same computer used to export datasets from VCell
- Start Plugins -> VCell -> “VCell Simulation Results Viewer”.
- The exports prepared in VCell will be visible in Personal Exports Table. You can also see sample export to try and test the plugin by clicking on Show Export Examples button top right.
- Select the dataset to see. Metadata (variables, changed parameters) are visible at the bottom. After clicking on Open button top right, the dataset will be open in ImageJ.
- By default, the Open in Memory is selected, and the file will open in the local computer memory. If the dataset is very large, you may uncheck the Open in Memory to view directly from the server without loading the file into your computer’s memory. This feature allows the user to view and analyze datasets that are too large to hold in memory. Note however, that changing views or using analysis tools can be much slower depend on your internet connection speed.
- Refresh the table after changing any of the filters or if you have exported new datasets from VCell.
- Copy Link copies the path to the VCell server location for the selected dataset. The link will allow other analysis software access to the data. The link can be shared with others and provides access only to the specific exported dataset.
N5 files store floating point values for concentrations or arbitrary units for convolved species. Use the Image -> Adjust ->Brightness/Contrast function to adjust the display appropriately. In addition to a channel for each species included in the exported results, an additional channel displays the volume structures in the simulation geometry as different pixel values.
View simulation results in Fiji/ImageJ on any computer using link
You can open the dataset that was exported by anyone else on any other computer. For that, the person preparing the export should click on “Copy Link” button next to the dataset of interest in VCell, and send the link to the person who will work on it.
- Click on Use N5 link
- In the pop-up window, paste the link and click on Open N5 URL
N5 files store floating point values for concentrations or arbitrary units for convolved species. Use the Image -> Adjust ->Brightness/Contrast function to adjust the display appropriately. In addition to a channel for each species included in the exported results, an additional channel displays the volume structures in the simulation geometry as different pixel values.
Release Notes
Version 0.1 – released July, 2024
The basic functionality for remote opening of VCell simulation results in ImageJ/Fiji.