Tool installation
Learning Objectives
After completing this lesson, learners should be able to:
Install the software that is required to execute the activities in this training material
Motivation
Provide instructions for installing the software required for this workshop. Please follow the instructions given by your trainer regarding which software you will need!
Concept map
Figure

Activities
Install ImageJ
Install the ImageJ GUI and a scripting editor.
Show activity for:
Fiji
Fiji bundles the ImageJ GUI, a scripting editor and various plugins available as optional update sites.
IntelliJ
IntelliJ is an IDE for developing Java code. It can be used to develop and run ImageJ code.
- TODO
- TODO
Install skimage & napari
Install the python library skimage for image analysis and the napari viewer for image inspection.
Show activity for:
conda
Installation (only once)
- install miniconda
- open a terminal window
- Windows: Anaconda Prompt (Miniconda3), e.g. type
Anaconda
in the search bar- write
conda create -n skimage-napari-tutorial -c conda-forge python=3.10 napari=0.4.17 notebook matplotlib jupytext "scikit-image>=0.20"
and press enter- create a directory called
skimage-napari-tutorial
(e.g. on your Desktop)- download OpenIJTIFF.py to the
skimage-napari-tutorial
directoryTest installation (only once)
- download test_installation_skimage_napari.py to the
skimage-napari-tutorial
directory.- open a terminal window (see above)
cd skimage-napari-tutorial
conda activate skimage-napari-tutorial
jupyter notebook
- Click on
test_installation_skimage_napari.py
. You will get a notebook with preconfigured cells. Run the cells one by one (Run
button orShift-Enter
). The napari GUI will show twice the same image.- create a new notebook
New > Python 3
- type following commands in a cell and execute the cell by pressing the
Run
button orShift-Enter
.# %% [markdown] # # Test python napari skimage install # %% # Instantiate the napari viewer import napari viewer = napari.Viewer() # %% # Read the intensity image from skimage.io import imread fpath = 'https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__two_cells.tif' image = imread(fpath) # %% # View the intensity image viewer.add_image(image) # %% # Read via OpenIJTIFF (OpenIJTiff.py must be in the same folder as the notebook path) from OpenIJTIFF import open_ij_tiff image_opentiff, axes, scales, units = open_ij_tiff(fpath) # View the intensity image viewer.add_image(image_opentiff)
Start (every time)
- open a terminal window (see above)
cd skimage-napari-tutorial
conda activate skimage-napari-tutorial
jupyter notebook
To run an activity either:
- (with package
jupytext
) create an empty file, e.g.current_activity.py
in theskimage-napari-tutorial
directory. Copy the activity code to this file and save the file. From thejupyter
main landing page click on the file.- Create a new notebook
New > Python 3
and copy the code in the activity into the notebook.
BAND
New BAND users
- Go to band.embl
- We recommend using Chrome or Firefox browsers. Please avoid using IE as it is not supported. Safari and Opera may be ok as well, but they are not thoroughly tested.
- Agree to the Terms of Use and Privacy Notice and click the “Login” button.
- We recommend Google authentication.
- After entering your credentials, check your emails for a confirmation email. It will typically take a maximum of 5 mins. Please also check your spam folder.
- Do not try to use the BAND before you receive the confirmation email.
- Please contact cbbcssupport@embl.de if you do not receive your confirmation email within 10 mins.
Once you receive your confirmation email, go back to band.embl.de and log in again.
You will be automatically redirected to the “Launch desktop” page after successful login.
- Please choose the following desired configurations (CPUs, Memory, GPUs, Screen resolution, and desktop running time).
- No. of CPUs = 1
- Memory (gb) = 2
- No. of GPUs = 0
- Resolution = your preference
- Time (days) = 1
Click “Launch Desktop”
- If you encounter an error launching a desktop, please contact us at cbbcssupport@embl.de.
- One user is only allowed to have 1 running desktop.
- Your desktop will be available in the ”Running Desktop” section if the launch is successful.
If this is your first time using the BAND, you may see a red error message appear after clicking “Go to Desktop”. If you see it, please simply stop the desktop and re-launch. The error is due to system and network limitations. It will go away, and the performance of your desktop will be optimal from your second desktop onwards.
If the “Go to desktop” button is greyed out, it means there are not enough resources available for your request. In this case, you have two options: 1) Stop your desktop and adjust your configurations. Lower the requested number of CPU, Memory, or GPU and launch again. 2) Wait until other users release their desktops so that more resources become available. The “Show Desktop” will automatically become clickable once there are enough resources.
- Click “Go to desktop” to view your desktop in a new browser tab.
- Click “SSH to Desktop” if you prefer a command-line interface.
Once your desktop appears in a new tab, you can access all the available software from the Application menu on the top left of your screen.
- After using your desktop, close the browser tab and click the “Stop desktop” button from the launch screen.
Existing BAND users
- Go to band.embl
- Click “Login” from the menu and then continue from step 5 above.
Launch skimage/napari
To execute the below steps you need to open a terminal window:
…and you also need to open an Application:
Open a Terminal and execute
- cd Documents # go to the Document folder - mkdir skimage-napari-tutorial # create a folder called skimage-napari-tutorial - cd skimage-napari-tutorial - wget https://neubias.github.io/training-resources/functions/OpenIJTIFF.py
Go to “Applications Places->Programming->JupyterLab”. Select ‘napari.tensorflow’ Kernel
Save the jupyter note-book file in skimage-napari-tutorial folder
File>Save Notebook As …> Documents/skimage-napari-tutorial/”FileName”.ipynb
We have napari from the menu. Or if you prefer to start napari within Jupyter, just type “%gui qt5” and ignore the warnings.
BAND tipps
- Do not run the “skill ” command, which may affect your running session and do not “scancel” the slurm job running your desktop session.
- Do not use any .bashrc in your home directory. It will cause the guacamole connection error.
- DO NOT store large files in /home, move or download large files to /scratch. If /home is full, BAND will break. THIS IS IMPORTANT.
- Refer to User guide for copy & paste instructions
- Use pure Google accounts or accounts that purely managed by Google. Account linking, for example, login with Hotmail with account linking to Google may not work.
- User data stored in /home and /scratch persists between desktop sessions. Stop desktop will not lose data.
- Recommend to log in to BAND at least once before the course. This is to give enough time to fix issues if there are any.
Explanations
Installation instructions
To visualise the installation instructions, please select the required platform in the activity list.
Follow-up material
Recommended follow-up modules:
Learn more: