Medical animations and surgical visualisation with MedFilm

Dion Moult
, 07/10/2018 | Source: thinkMoult

You’re sitting in front of the doctor’s table in a hospital. The doctor has just spent the past half hour explaining the procedure you will undergo to solve a medical problem that you experience. It sounds complicated — there are a few things you have to do to prepare, some foods to watch out for, and a recovery process of a few months afterwards. You will later come home to only be bombarded with a series of questions from your friends and family, who are all curious and have somehow managed to ask the questions which you didn’t think of asking earlier. It also doesn’t help that their native language isn’t English.

Four years ago, this was exactly the problem that Erik Kylen, a small team in Sweden, and myself working remotely set out to solve. The solution was a series of animated videos to explain various medical issues in simple terms. A doctor could use these videos to help guide patients, and patients could then watch these videos from the comfort of their own home. This is MedFilm.

MedFilm Logo

Each video starts with a gentle description of the various body parts involved in the procedure to introduce the required medical terminology. This is followed by an explanation of how these parts relate to the ailment at hand. The patient is then reminded of the various preparatory steps they need to take before the procedure, such as fasting, or drinking fluids. The surgical procedure is then shown, heavily tested to maintain medical accuracy whilst ensuring that the patient does not see anything gruesome. Finally, the video describes the recovery process, and the steps the patient can take to expedite it.

These videos are simple to understand, are accessible with subtitles and translations into many languages, and tailored for specific medical practices in localised hospitals and countries. Each hospital and country has their own preferred ways of doing things, and these videos accomodate that fact.

A doctor from a participating hospital can share a link to their patient, or interactively use the video during the briefing process on a tablet. A patient can later watch it again to refresh their memory, or reshare it with friends and family.

MedFilm surgical videos on various tablets

Let’s see a demonstration video (and yes, videos can be embedded with custom branding into a hospital or clinic’s website!). Below is the video created for an appendectomy. Usually, getting your appendix removed is a pretty safe, standard procedure, and happens pretty soon after you figure out you have a problem. Most people have also heard of it, which makes it a great procedure to demonstrate.

Here’s the video! Click play below and learn about an appendectomy!

MedFilm is steadily growing and now has a repository of 40 videos covering topics from cardiology to otorhinolaryngology (I’m not a doctor, so to me that’s a very complicated word!), used in clinics across Scandinavia. I’m proud of the service, and happy that it is able to help patients. If you’re interested are are involved in the health industry, you can contact MedFilm here and we can explore opportunities!

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Penetration testing on AWS

In opposition with the general assumption, among companies which have a long compliance history in their field, top executives are often the most eager to migrate their On-premise infrastructure in favor of Public Cloud, expecting1 drastic operational cost savings. The opposition more often comes from the IT Operations and Security staffs who fear a loss of control on their data which goes along with the loss of control on the underlying infrastructure ( They miss Network and Security appliances, Hypervisors and sometimes even Racks and Wires 😏 ).

Mining on AWS

WARNING: THE METHOD DESCRIBED IN THIS ARTICLE IS ONLY TARGETING PEOPLE WHO HAVE AWS CREDIT TO LOOSE, DON’T USE IT WITH PROFITS IN MIND Considering cloud instances are usually expensive, and price of cryptocurrencies ( and especially the ones that are still minable with CPU and GPU ) are collapsing lately, most of you must think I’m turning mad. And, indeed, the target of this walkthrough is absolutely NOT BEING PROFITABLE.

An Introduction to Risk Analysis

An Introduction Far from proposing you a full formation to ISO 27005, this short post will introduce to you the basis to keep in mind before starting any new Security Project. Indeed, contrary to other investments, security won’t bring new value to your company Business; instead, it gives you the promise to protect your current value. As I’ve already discussed with students in a recent lecture, I gave on the Risks of IT Outsourcing, when you subscribe to a new outsourcing contract, concerning security, the External Service Provider (ESP) has an obligation of means he should apply rather than results.

Worldwide GPS tracks with OpenStreetMaps for urban design analysis

Dion Moult
, 03/07/2018 | Source: thinkMoult

I work as an architect, and one of the data available to us when masterplanning and early phases of an urban design project is GPS track activity. Knowing where people drive, where people walk, and cycle and recreate allows us to make decisions such as where to define architectural axes, where to place retail, and how to extend public transport and pedestrian walkways.

One of the resources available is from a company known as Strava, who runs a proprietary fitness social network, where fitness buffs can track their movements via GPS devices (which can be as simple as your phone) and compare cycling routes, distances run, and so on. Primarily used by runners and cyclists, these GPS logs are voluntarily uploaded to Strava, who then aggregates all the data and resells it to urban design parties, known as their “Strava Metro” initiative.

Publicly without purchasing any data, Strava also hosts a global GPS heatmap where you can visually see the fire of activity by runners and cyclists. Zooming in shows you right down to where people run down various streets. As a high-level overview, this is a great graphic and can immediately pinpoint activity. It also is a fantastic feat of engineering, processing 5 terabytes of raw input data. That’s big data!

Strava heatmap example

Of course, just recently Strava decided to stop showing this public heatmap at high zoom levels and locked it behind a paywall. Thankfully, there are alternatives.

In a previous post, I introduced an open-data initiative known as OpenStreetMaps. Strava is largely based on OpenStreetMaps and uses it as a base layer embedded into MapBox, and also has a fork of the OSM iD editor called “Strava Slide”, to allow people to edit routes based off strava GPS data tracks. However, OSM itself has many active GPS track contributors (used for various purposes, such as mapping new routes and calibrating the map), and we can use this open data in lieu of the proprietary product offered by Strava. Below, we see the world’s GPS tracks from the perspective of OSM visualised by Pascal Neis.

OSM GPX tracks

Before I get into the specifics of getting GPS data, I’d like to show you what data is in a GPS track. Here’s some GPS tracks visualised with JOSM. We can see things like speed, direction, and sometimes, elevation, if it is recorded. See those red segments of the line? Those are traffic lights!

GPS track velocity visualised with JOSM

OSM has an API and Planet GPS extract available to download GPS data. The Planet GPX is rather unwieldy, and is also very outdated (from 2013). The API is not the best either, in that it only returns 5,000 GPS points per query, and doesn’t quantify the total pages of results, so that you can’t really tell with one query how many points you need to fetch in advance. However, if you query the API and put a page number higher than what is available, it won’t return any points. So using a binary search you can find out how many pages to extract.

For the area of Sydney, there are roughly 750 pages of results, so that means just under 4 million GPS points. Here’s a heat map visualisation of it I made using QGIS (but JOSM also has a heat map visualisation feature). You won’t need huge supercomputers processing the data, either.

Sydney, Australia GPS activity heat map

Here’s another of Manhattan, New York.

Manhattan, New York, GPS activity heat map

We can couple this visualisation with other OSM data such as all public transport nodes. In this case, railway tracks, bus routes, ferry routes, cycling routes, train stations, and bus stops are shown. This is also created with QGIS.

Sydney public transport GPS analysis

There are a few pros and cons to using this GPS data. The pro is that it’s more general purpose: it’s not only used by runners and cyclists, it’s used by regular people (well, GIS geeks) doing everyday things like shopping. Unfortunately, OSM isn’t that widely used, and so the data is relatively sparse. In remote areas perhaps no-one has walked that route, or only a few people have. So you don’t get a sense of what they’re doing. The GPS data is also not processed, so you’ll have to do your own cleaning: especially in the city where GPS data goes a bit haywire with all the tall buildings.

Have fun and happy mapping!

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Edmondson Park – a retail and residential development by Frasers and HDR

Dion Moult
, 24/06/2018 | Source: thinkMoult

Three weeks ago, 30 kilometers away from the Sydney city centre in the rural suburb of Edmondson Park, Frasers Property Australia opened the doors of their display centre to the public. This brand new town centre development with residential and retail environments was designed by HDR Inc, of which I am part of the team of architects. I haven’t really talked much about my architecture work before, but a brand new town centre in a previously uneventful part of Sydney is perhaps worth a blog article.

Perhaps let’s start with the blurb of the development which I’ve copied directly from the Frasers official Ed Square website:

From the makers of Central Park Sydney, Ed.Square brings inner city edge, but with so much more than you expected.

Ed.Square is a diverse urban neighbourhood of restaurants and cafes; shopping and entertainment; playgrounds and parklands; a market place and Eat Street; adjacent to the Edmondson Park train station and all within walking distance from your own front door.

Ed offers an array of residences crafted by some of the worlds best architects that cater for every lifestyle. Whether you are a first home buyer or a multi-generational family, you’ll always feel at home with Ed.

Sydney’s South West is one of Sydney’s growth trajectories, and so the Edmondson Park development is one of those which will supply the population growth.

Despite working on the development, I probably don’t have any permission to use any marketing material, so you’ll have to visit the Frasers website to see all the pretty pictures and marketing.

However, I did take some snaps of the display suite, so here it is! Let’s start with the view you get as you enter. To the left are some display town houses. They are three storey products which surround the town centre. If you use some imagination you can read that there is the huge word “Ed.” written in bright yellow in front of it. Ed’s pretty hip, and is the anthropomorphism of the neighbourhood. To the right, you can see a cafe by the display centre itself, which apparently serves some pretty tasty dishes that the local community loves — but it was closed when I arrived.

Edmondson Park display village centre

Here’s what you see as you enter…

Edmondson Park display suite entrance

And a snap of the physical model…

Edmondson park model

Let’s zoom in! The orange letter “T” is the train station, so you can see that the town centre is literally adjacent to it. The white buildings have yet to be released, so stay tuned.

Henderson Road model shot

Here’s another angle, showing the grand cinema facade.

Edmondson Park cinema

There’s a display apartment too …

Edmondson Park display apartment

… which shows some of the apartment, such as this fancy kitchen.

Kitchen in display apartment

Here’s another view from the balcony of one of the town houses looking at the display suite. In the background you can see a huge pit where construction will occur, surrounded by Cumberland Plain Woodland. I hear there could be koalas living there.

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If you live in Sydney, feel free to drop by!

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OpenStreetMaps – an open-source Maps application

Dion Moult
, 19/06/2018 | Source: thinkMoult

Recently I’ve been interested in an initiative known as OpenStreetMaps. Launched in 2004, OpenStreetMaps is the open-source equivalent of Google Maps, and functions largely like how Wikipedia does (and in fact was inspired by Wikipedia) – it’s a map of the world drawn completely by volunteers and open-source enthusiasts.

OpenStreetMaps world map

You might’ve already seen OSM in action. Below it’s used by default in the privacy-friendly search engine DuckDuckGo, other wiki-based projects like WikiVoyage, and many games use it as a base layer, such as Pokemon Go.

PokemonGo uses OpenStreetMaps as a base layer

You’ve probably used Google Maps before and have it installed on your phone to help you drive to places with the GPS. You may have also played with Bing Maps which essentially does the same thing. At first glance OpenStreetMaps is purely a clone: you can zoom in and out, look at street names and see buildings, and have it tell you how to drive to a destination. It’s not that exciting, and isn’t worth talking about.

However if you were a user of OSM, occasionally you might notice areas of the map where volunteers have gone above and beyond to draw details of the environment that other maps will not. Things like individual driveways, articulated building outlines, kerbside grass, wheelchair accessible walkways and kerb ramps, and individual bush and tree locations, fences, and parking niches. Zooming in we can identify storm drains, streetlamps, water taps and park benches. This level of detail is possible because the map is created by people who are genuinely interested and express a love and care in their work. The example below is in Brisbane, Australia, largely by a fellow called ThorstenE.

OpenStreetMaps example in Brisbane, Australia

Where OSM really excels is as an open-data resource. Usually, you are only limited to raster map images produced by Google Maps and Bing, but aren’t allowed to access the underlying database of geographic and vector information. In contrast, because the data in OSM’s database is free for everyone, specialist maps can easily be created. Take for example the extensive mapping of skiing and snowboarding tracks in Oslo, Norway provided by OpenSnowMap

OpenSnowMaps

… alternatively there is the Whitewater rafting map in the UK …

Open Whitewater Rafting maps

… and the OpenCycleMap which maps the world’s bicycle routes, and shows the incredible culture of pedestrian and cycling friendly urban planning in the Netherlands.

OpenCycleMaps example

OSM also helps lead the way in humanitarian mapping. When a flood, fire, earthquake or other natural disaster occurs, existing maps provided by Google and Bing are no longer current. Mappers need to create new maps to allow disaster relief teams to coordinate their efforts, target houses for rescues efficiently, or to know what routes relief organisations can take to navigate the terrain. This work is done by the excellent Humanitarian OpenStreetMap Team. It also includes non natural disasters, such as mapping demographics and environmental issues related to poverty elimination, gender equality, refugee response strategies, public disease outbreaks, clean energy, and water and sanitation. As one current example, right this minute the Monsoon rains have caused severe flooding in the Kurunagala and Puttalam districts of Sri Lanka. A map is being prepared so that first respondents and aid agencies can deliver relief supplies. A grid of zones with their mapping progress is updated in real time below.

Humanitarian OpenStreetMaps Team map in Nepal

As an open-source creation, it doesn’t data-mine your activity so you can use it as a Maps application without privacy concerns, you can download the raw vector so you can use it offline on your phone, and has a conservative approach to licensing data that allow people who want to embed OSM technologies in their own creations in a much more flexible manner. If you feel strongly about supporting privacy-aware applications (especially after the Cambridge Analytica scandal), and encouraging communities that aren’t motivated by profit, OpenStreetMaps should be something to consider. There are over 1,000,000 mappers who have contributed to OSM, and you can become one of those too.

One of the most amazing things about OSM is that whereas mapping the world is an inherently complex process, it has managed to make it easy and fun and doable by anybody who knows how to draw a rectangle with their mouse. Most of the other open-source initiatives have a high learning curve and lots of technical prerequisites, but OSM is completely the opposite. Just zoom into your city on OSM.org and click the Edit button on the top left. It will give you a short tutorial that lets you draw new roads and buildings within minutes. The thought that has gone into the user-friendliness of this online map editor is absolutely incredible.

OpenStreetMaps iD web-based editing software

I’ll talk about OSM a bit more in upcoming posts, and share some of the more interesting technical sides of things.

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The three container security golden rules

As containers became a standard in IT applications, enumerating a few security best practices is now a business need. Therefore I’ve defined those three golden rules to keep in mind before pushing a new image for production to your company container repository. I Careful with share volumes you will be Contrary to a Virtual Machine, a Docker container uses the host kernel directly, so in case of a kernel vulnerability restricted permissions on shared resources won’t protect you from an attacker.

Secure your site with Lambda@Edge

Let’s now deal with a more enjoyable subject. In my precedent posts, it was essentially related to Sysadmin aspects, I wrote those articles as I wasn’t able to find any satisfyingly complete reference online, so I’ve decided to write them. However, you probably see in my description corner that I am an Amazon Web Services certified, adept of DevOps and with a strong focus on the security aspects. As I’ve got freshly, AWS Security Specialty certified, it was high time I approached an AWS security oriented subject; I’m not going to describe how I’ve built and deployed this website, I myself found all the needed information here.

Ship your Applicative log files anywhere

As I recently had to manage an integration project for the Security Operation Center service of a big company, I had to configure applicative logs forwarding to the nearest SIEM syslog collector for each service included in the scope. I’ve found that the rsyslog agent is usually preinstalled in any Unix distribution with default operating system log folders configured out of the box so that the system log forwarding is most of the time almost as simple as service rsyslog start 1.