Learn Pathology

Learn Pathology is a web-based system for teaching students the field of pathology. In the system, teachers can create online courses and assignments. Students can view and interact with large whole slide microscopy images (WSIs) as well as answering questions and performing assignments.

Learn Pathology is developed by the Norwegian University of Science and Technology (NTNU) and SINTEF Digital, the Health Department, and is released under the permissive MIT license.

The system is built using the following open source technologies:

• Django
• OpenSeadragon
• FAST
• OpenSlide

Requirements

• Python 3
• For FAST backend you must have OpenCL installed

Development setup

This is for setting up and running learn pathology locally on your computer for development purposes. For deployment of the system on a web server, see the deployment instructions below.

1. Clone project

git clone https://github.com/AICAN-Research/learn-pathology.git
cd learn-pathology

2. Create virtual environment

# Install environment
pip install virtualenv
virtualenv -ppython3 environment
# Activate environment
source environment/bin/activate # Linux
environment/Scripts/activate.ps1 # Windows
# Install dependencies
pip install -r requirements.txt

3. Create database

python manage.py migrate

4. Create super user

python manage.py createsuperuser

5. Run server

python manage.py runserver

Open your web browser at http://localhost:8000

6. Add some slides

• Download some slides from http://openslide.org/demo to your machine
• Login
• Go to admin page
• Press slide, and add some slides to the database

Deployment & Server optimization

This guide is for Ubuntu Linux. To setup Learn Pathology for deployment on a server use apache2 and mod_wsgi.

1. First install packages

sudo apt install python3-pip apache2 libapache2-mod-wsgi-py3

Also make sure you have all requirements for FAST installed:

sudo apt install libgl1 libopengl0 libopenslide0 libusb-1.0-0 libxcb-xinerama0

You also need OpenCL. To install OpenCL on Linux, download an implementation depending on the CPU/GPU you have.

2. Then clone the repo on the server for instance to /var/www/

cd /var/www/
git clone https://github.com/AICAN-Research/learn-pathology

3. Setup virtual environment on the server

cd learn-pathology
virtualenv -ppython3 environment
source environment/bin/activate

4. Install requirements

pip install --upgrade pip # Make sure pip is up to date first
pip install -r requirements.txt

5. Create a secret key and configure settings
Generate a secret key and add it to settings.py

python manage.py shell -c 'from django.core.management import utils; print(utils.get_random_secret_key())'

Edit the file learnpathology/settings.py. Uncomment and set the SECRET_KEY to the output of the python command above. Remember to keep this key secret, and do not push it to git/github. You may change it, even when the system is in use, but note that users may be logged out. See here for more info: https://medium.com/@bayraktar.eralp/changing-rotating-django-secret-key-without-logging-users-out-804a29d3ea65

Disable debug mode by setting debug = False. For security reasons this should always be off on a production server, only turn it on if you need to actually debug.

Add your domain to ALLOWED_HOST, for example like so:
ALLOWED_HOSTS = ['learnpathology.no', 'www.learnpathology.no']

6. Initialize database

./manage.py makemigrations
./manage.py migrate

7. Create super user

./manage.py createsuperuser

8. Collect static files

./manage.py collectstatic

9. Fix user permissions
Apache needs write access to the database. Apache runs on the user wwww-data thus give this user write access to the root folder and the database file db.sqlite3

cd ..
sudo chown :www-data learn-pathology
sudo chmod g+w learn-pathology
cd learn-pathology
sudo chown www-data db.sqlite3
sudo chmod g+w db.sqlite3

10. Create an apache config

sudo nano /etc/apache2/sites-available/learnpathology.conf

You should always use HTTPS and SSL encryption. If you are not using HTTPS, you are essentially transferring everything, login password, images, on the webpage totally unencrypted over the internet! To use HTTPS/SSL encryption you need an SSL certificate, you can buy one cheap from services like namecheap.com or free from Let's encrypt. Store the certificate, the key, and the CA certificate files on the server, e.g. in folder /var/www/learn-pathology/ssl/. The config with SSL/HTTPS end-to-end-encryption will then look something like this:

# Redirect to secure site
<VirtualHost *:80>
    ServerName learnpathology.no
    ServerAdmin [email protected]
    Redirect permanent / https://learnpathology.no
</VirtualHost>

<VirtualHost *:443>
    # Common stuff
    ServerName learnpathology.no
    ServerAdmin [email protected]
    DocumentRoot /var/www/learn-pathology/

    # SSL stuff
    SSLEngine on
    SSLCertificateFile "/var/www/learn-pathology/ssl/certificate.crt"
    SSLCertificateKeyFile "/var/www/learn-pathology/ssl/certificate.key"
    SSLCACertificateFile "/var/www/learn-pathology/ssl/certificate.ca.crt"

    Alias /static /var/www/learn-pathology/static
    <Directory /var/www/learn-pathology/static>
        Require all granted
    </Directory>

    <Directory /var/www/learn-pathology/learnpathology>
        <Files wsgi.py>
            Require all granted
        </Files>
    </Directory>

    # Modify this to fit your python version:
    WSGIDaemonProcess learnpathologywsgi python-path=/var/www/learn-pathology/:/var/www/learn-pathology/environment/lib/python3.10/site-packages processes=32 threads=32
    # This setting is needed for FAST to run properly:
    WSGIApplicationGroup %{GLOBAL}
    WSGIProcessGroup learnpathologywsgi
    WSGIScriptAlias / /var/www/learn-pathology/learnpathology/wsgi.py

    ErrorLog ${APACHE_LOG_DIR}/learnpathology.error.log
    CustomLog ${APACHE_LOG_DIR}/learnpathology.access.log combined
</VirtualHost>

11. Enable website and test

sudo a2ensite learnpathology
sudo systemctl reload apache2

Open your browser and check that the webpage works. A usual cause of error on the apache2 server, when enabling the website, is a syntax error in the configuration file. In such situations, you can use the command line apache2ctl configtest to debug the file.

12. Server Optimizations

Use mpm_worker to enable multi-processing and multi-threading

By default, apache will use mpm_prefork to handle multiple requests, which do not use any multi-threading. If you plan to serve hundreds of simultaneous users, you should consider using mpm_worker instead.

To do so, first enable mpm_worker:

sudo a2dismod mpm_prefork
sudo a2enmod mpm_worker
sudo service apache2 restart

Then open the mpm_worker config: sudo nano /etc/apache2/mods-enabled/mpm_worker.conf

The following config has worked well for us:

<IfModule mpm_worker_module>
        ServerLimit              32
        StartServers             16
        MinSpareThreads          50
        MaxSpareThreads          100
        ThreadLimit              64
        ThreadsPerChild          50
        MaxRequestWorkers        512
        MaxConnectionsPerChild   0
</IfModule>

Restart apache after changes:

sudo service apache2 restart

Enable turbojpeg

Requested image tiles have to be compressed with JPEG before they are sent to the users. By default, PIL is used for compression which is slow. Turbo JPEG is a faster option.

To use TurboJPEG, first install it:

sudo apt install libturbojpeg

and install it in your python environment:

pip install PyTurboJPEG==1.7.*

then enable it in learnpathology/settings.py:

USE_TURBOJPEG = True

Reload apache after changes:

sudo service apache2 reload

Cache tiles in memory using memcached

In an educational setting, you might have several hundred students which will access the same few images at the same time during class. Since reading images from the harddrive is one of the slowest operations, you can considerably improve performance by having the images in memory instead. In this case, all students, except the first one, accessing an image, will read images directly from memory instead of the slow harddrive.

We recommend using memcached for this purpose, you can install it like this:

sudo apt update
sudo apt install memcached libmemcached-tools
sudo service memcached start

Modify memcached config to allow it to use a lot of memory and large enough objects to be stored: nano /etc/memcached.conf:

# Depending how much RAM you have, set the limit of you much
# memory memcached should be allowed to use, here we have set it
# to 100 GB = 100*1024 = 102400 MB:
-m 102400
# Allow file sizes up to 3 MB
-I 3m

Restart after modifying the config:

sudo service memcached restart

Install the pymemcache binding in your python environment:

pip install pymemcache==4.*

Enable the tile caching in learnpathology/settings.py:

USE_TILE_CACHE = True

Reload apache after modifying settings:

sudo service apache2 reload

You can check if memcached is working by looking at its statistics (how many items are stored, number of cache hits/misses etc.):

memcstat --servers="127.0.0.1"

The images are stored for 30 minutes in memory as defined in slide/views.py:

@cache_page(60 * 30)
def tile(request, slide_id, osd_level, x, y):
    ...

Learn Pathology is set to store a maximum of 100 000 images, here are the settings we have used (defined in learnpathology/settings.py):

if USE_TILE_CACHE:
    CACHES = {
        'default': {
            'BACKEND': 'django.core.cache.backends.memcached.PyMemcacheCache',
            'LOCATION': '127.0.0.1:11211',
            'MAX_ENTRIES': 100000,
            'OPTIONS': {
                'no_delay': True,
                'ignore_exc': True,
                'max_pool_size': 4,
                'use_pooling': True,
            }
        }
    }

13. Setting up FEIDE login

To enable users to login using FEIDE/dataporten make sure you have got your client ID and secret key from your local FEIDE administration.

Then enable FEIDE login in learnpathology/settings.py:

USE_FEIDE_LOGIN = True

Reload apache after modifying settings:

sudo service apache2 reload

Then go the admin page using your browser and create a new item under "Social applications" and set the provider to Dataporten and enter your client id and secret key, also remember to add a site and select it with your domain.