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Welcome!
If you are here, it means you are interested in performing image analysis on O2 with the data you've acquired. We have prepared installers specifically for HMS O2 users, featuring heavily utilized image analysis tools. Our goal is to simplify your workflow as much as possible.
To alleviate the hassle of complex installation processes, we have developed bash scripts that manage all necessary dependencies behind the scenes. Installation is straightforward: simply log into O2 and run a single command to install the software you need. After installation, the script generates an executable desktop file for easy software launching. A key advantage of our system is its persistence—any installations or modifications, such as plugins you add, will remain in your local directory even after you log out.
We hope these tools prove useful and significantly enhance both your image analysis capabilities and your scientific discoveries!
- Fiji / ImageJ
- QuPath 0.5.1
- Cellpose 3.0
- Napari
- Ilastik
- Plantseg
If you have a software request, please feel free to contact us.
- Use the instructions below to log in to a login node:
- Using terminal on local computer: You can find a comprehensive instructions provided by RC here on how to use a terminal to SSH into a login node. Depending on the operating system on your laptop, you may need to perform different steps.
- Using a browser (Chrome recommended): Alternatively, you can also go to this link to login to an O2 shell via browser. Detailed instructions are provided here.
- Once you log in, run the following command to request compute access:
srun --pty -p interactive -t 0-4:00 --mem 16g bash
Fiji / ImageJ
/n/app/bias/fiji-imagej/fiji-imagej.sh -i
or
/n/app/bias/fiji-imagej/fiji-imagej.sh --install/n/app/bias/fiji-imagej/fiji-imagej.sh -u
or
/n/app/bias/fiji-imagej/fiji-imagej.sh --uninstall/n/app/bias/fiji-imagej/fiji-imagej.sh -h
or
/n/app/bias/fiji-imagej/fiji-imagej.sh --help
QuPath
/n/app/bias/qupath/qupath.sh -i
or
/n/app/bias/qupath/qupath.sh --install/n/app/bias/qupath/qupath.sh -u
or
/n/app/bias/qupath/qupath.sh --uninstall/n/app/bias/qupath/qupath.sh -h
or
/n/app/bias/qupath/qupath.sh --help
CellPose 3.0
/n/app/bias/cellpose/cellpose3.sh -i
or
/n/app/bias/cellpose/cellpose3.sh --install/n/app/bias/cellpose/cellpose3.sh -u
or
/n/app/bias/cellpose/cellpose3.sh --uninstall/n/app/bias/cellpose/cellpose3.sh -h
or
/n/app/bias/cellpose/cellpose3.sh --help
Napari
/n/app/bias/napari/napari.sh -i
or
/n/app/bias/napari/napari.sh --install/n/app/bias/napari/napari.sh -u
or
/n/app/bias/napari/napari.sh --uninstall/n/app/bias/napari/napari.sh -h
or
/n/app/bias/napari/napari.sh --help
Ilastik
/n/app/bias/ilastik/ilastik-1.4.0.sh -i
or
/n/app/bias/ilastik/ilastik-1.4.0.sh --install/n/app/bias/ilastik/ilastik-1.4.0.sh -u
or
/n/app/bias/ilastik/ilastik-1.4.0.sh --uninstall/n/app/bias/ilastik/ilastik-1.4.0.sh -h
or
/n/app/bias/ilastik/ilastik-1.4.0.sh --help
PlantSeg
/n/app/bias/plantseg/plantseg.sh -i
or
/n/app/bias/plantseg/plantseg.sh --install/n/app/bias/plantseg/plantseg.sh -u
or
/n/app/bias/plantseg/plantseg.sh --uninstall/n/app/bias/plantseg/plantseg.sh -h
or
/n/app/bias/plantseg/plantseg.sh --helpOnce the installation is complete, you can verify that everything is set up correctly by logging into Desktop Mate. If you're unsure how to do this, please refer to this HMS RC guide on logging into Desktop Mate. We recommend using at least 16GB of memory for optimal performance. If you're working with larger images or tasks that require more resources, please allocate additional memory as necessary.
Upon logging in, you'll find an icon on your desktop displaying the software’s logo and name. To launch the software, simply double-click this icon. The software is permanently installed on our Desktop Mate environment, meaning you only need to install it once. It will remain available for future sessions, just like software installed on your local computer.
When you're finished using the software, you can log out. The next time you need it, just log back in, and it will be ready to use again.
How does the installation work?
The bash scripts handle the installation of various bioimage analysis tools differently. For Fiji, QuPath, and Ilastik, it downloads the compressed files, extracts them into the Documents folder, and creates an executable on your Desktop. For Cellpose, PlantSeg, and Napari, the process is a bit more nuanced. The script sets up separate conda environments for each, installs the required packages, and then creates a dedicated folder in the Documents directory. It writes a Bash script in this folder that, when executed, activates the corresponding environment and launches the software. Finally, it generates an executable file on the Desktop for easy access.
How do I use data stored on our lab’s shared drive?
To access any data that’s on O2 (individual scratch, shared scratch, shared group folder, etc.), you first need to click on the checkboxes when you request Desktop Mate to access the storage. You can then go to Open folder → Computer → / → n
Once you go to n, you will see all the folders. Next, you can follow the path trail to your folder.
Where are the installation files stored?
The installation files are stored inside the Documents folder.
Can I use QuPath headlessly?
Yes! QuPath has instructions on how to use it headlessly on this FAQ page. Specific subcommands can be found in this sub-section. For O2 specific installation, the QuPath executable file can be found at ~/Documents/QuPath/bin
Does QuPath use GPU?
By default, QuPath does not use GPU and only StarDist can take advantage of GPU access right now. You can find more information regarding that here.
Can I use CellPose headlessly?
Yes! You can find necessary information regarding that here. For the CellPose executable, you will need to activate the CellPose environment first. You can do that using the following commands:
module purge
module load miniconda3/23.1.0
source activate cellpose
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