Clustering with MAfalda

I have recently been using the MAfalda framework (link) to work with my Timepix data. MAfalda is a framework build on top of root that simplifies the process analyzing Timepix data. It has a number of cool features, not least those offered by Root (serialization, intelligent file IO, trees and decent plotting features). With a bit of hacking around it possible to do some pretty cool stuff. For example below I am running a clustering algorithm and pushing the different clusters into different windows for an online look at the data.

EU Commisioner Visit To CERN

Last week Androulla Vassiliou, European Commissioner for Education, Culture, Multilingualism and Youth visited CERN. As part of this visit a poster session was organized where all of the Marie Curie programs at CERN were presented.

Brewing!

Last weekend I made a trip back to the UK to see some old friends. While I was there we seriously upgraded Chris beermaking setup with proper plumbing, a DIY electric boiler, a new pump system and a PID temperature controller. The next step is clearly a series of sensors and a ROOT interface. Warning, dubious electrical safety ahead...

New Lab!

After several months the lab next door is finally complete!

Timepix Wafers

I saw a Timepix wafer today at a clean room at CERN, fresh from fabrication at IBM. I also learned a fun (...) fact, Timepix chips are typically named something like I04, F10, and similar. This refers to their physical position (column and row) on the wafer.

ARDENT Visit to CERN

The ARDENT ESRs came to CERN today for a meeting. As part of this I arranged a trip down to the ATLAS cavern to see the detector.

Flat White Success!

We have had a Gaggia Unica super-automatic coffee machine in the office for a few months now. It makes a reasonably nice espresso (miles ahead of the CERN cafeteria at any rate) but steaming decent milk on it for a nice Flat White (a short, strong milky Australian confection) in the morning has always eluded me. Turns out the trick is to remove the little plastic widget at the end of the steam wand, suddenly I could make pretty good foamed milk (as opposed to the gloppy froth from before).

Pretty Graphs in ROOT

ROOT can make some very pretty graphs if you play with it (these ones are of spins states in a hexagonal Ising model).

Holidays and Neutrons

I spent a few weeks this month on holiday moving around Europe, in total we hit six countries, drank some good coffees (I can tick the Greek Frappe and Neopolitian espresso off the hit list) and generally loafed around. I also took some measurements with a Timepix and a neutron source at the end of the month when I got back to CERN.

Upcoming Secondment in Wollongong

I will starting a 2 month secondment at the University of Wollongong this month. While there I will work on Geant4 simulations of the Timepix system (specifically for neutron detection).

Work and play in Wollongong

Some pictures of Wollongong, including some measurements with a Timepix taken at a photon linac.

Even after a year, Timepix can still surprise me

Before calibration the Timepix can be a little tricky. For example shown below is the TOT spectrum of an Americium source. Notice that there are three peaks in the uncalibrated spectrum but only two when calibrated.

If we break the spectrum up into where the hits came from, the origin of the third peak becomes visible. Its from two pixel hits before they are calibrated. Its obvious when I think about it, but it shows how even a simple energy calibration can improve your data.

Shell Scripting...

Terrible puns abound in computer science. At least I know regular expressions now...

Tea!

As a proper Englishman I drink it builders strength with milk in a mug that declares my allegiance to salty yeast based spreads.

What a coincidence!

I spent a few hours this afternoon playing with the external triggering electronics on the FITPix box with some colleagues in Wollongong. The idea was to get both detectors triggering in conincidence. Seems to work pretty well.

Return to CERN and the Open Days

I am now back at CERN for the open days (which I spent Saturday afternoon volunteering for). I got a great view of Mt Blanc (a common occurrence when approaching Geneva Airport from the south it has to be said) on the way over.

Second ARDENT workshop

Went to the second ARDENT workshop at the Politechnico di Milano. We ran an outreach event on various radiation detectors with local schoolchildren which was a lot of fun. I also gave a talk on my research. Milan isn't the most interesting city from a tourism point of view, but it does have an abundance of nice restaurants and is a lot of fun.

IEEE NSS MIC Conference

Off to the IEEE NSS MIC conference (where I have a presentation) in Seoul, Korea. Korea is a fantastic town with an abundance of good food (if you like Kimchee anyway). I also went to a cat cafe which was a novel experience.

As seen at Geneva Airport

Proton Therapy Measurements in Trento

Off to a proton therapy facility in Trento, Italy for measurements with EURADOS. Trento is a really pretty town in the Dolomites, it has quite a unique mix of German and Italian culture - think huge great beer halls serving pizza and pasta.

Medipix Measurements at Legnaro National Lab

Testing some different converters at a neutron beam at INFN Legnaro. INFN Legnaro is quite a nice little place that always seems to be perpetually foggy. Also the cafeteria is fantastic...

Holiday Travels

Time for some holidays. We hit Dubai, Bangkok, Phuket, Chiang Mai and Hong Kong.

More tests at Legnaro

Back to INFN Legnaro for more tests.

CERN in the Evening

Beam Time at CNAO

Off to CNAO to test the Gempix (a new detector with a CMOS ASIC to readout a gas electron multiplier) for beam monitoring. CNAO is a hadron therapy facility in Pavia, Italy. They have a synchrotron so they can deliver both carbon and proton ion beams.

Clean Lab

A clean lab is a happy lab... Or something.

Back to Wollongong

Back to Wollongong for two weeks. Here is something new, multilayer plastic converters 3D printed for the medipix, the idea with these is that they mimic some response function when you integrate over the whole chip. Time to see if they work.

Back to CNAO

Back to CNAO. Turns out the restaurant next to the hotel we stay in in town is quite good. These things matter after you've spent 16 hours in a small room underground.

English Breakfast

I've you've ever wondered what a full english breakfast should look like, the answer is this (taken at Fagins in Sheffield).

60th Anniversary Open Days

Open days at CERN. We had a stall on medipix at CMS (shown below is Alvin explaining the wonders of the universe). As part of this I finally did the CMS tour. CMS is a smaller detector than ATLAS but in a similar sized cavern. Because of this you can walk around the detector and get a more comprehensive view of it. I have to say that it is much prettier than ATLAS.

Parking

As seen outside restaurant 2. No comment.

Back to CNAO - Never Blindly Trust GPS...

Never trust GPS. The one built into our rental though that this road was preferable to the Autoroute. It wasn't. The rest of the beamtime was a success.

Quad Timepix ASIC

Here is something fun, a naked quad timepix ASIC. Normally these are covered in a seamless silicon sensor so you can't see the gaps (although the pixels at the border are bigger so they count higher), but for the Gempix we don't need a sensor.

Vulcan Bomber

As seen at London Southend Airport while travelling through. This one is apparently the only airworthy specimen.

Geneva

Geneva is a very photogenic city, especially on a sunny, summers day.

Off to Texas

Off to an extended secondment with the University of Houston and the NASA space radiation analysis group. NASA have six Timepix units on the International Space Station that they use to do charged particle dosimetry.

Rockets

Of course there are rockets at Johnson Space Center in Houston. Lots of rockets.

Mission Control

Mission control and the radiation console at NASA JSC.

Apollo Mission Control

Apparently these are the original machines from back in the day. Seeing this stuff was amazing, I grew up on a diet of rockets and moon landings. Covered in an assortment of buttons these are obviously not computers in the way I am used to thinking about them. That these took men to the moon and back is amazing.

WORMISS in Krakow

Off to give a talk at WORMISS (Workshop on Radiation Monitoring on the International Space Station) in Krakow, Poland. This is the second time I’ve been to Krakow, and its been just as fun as the first.

Auschwitz

I took the opportunity to visit Auschwitz which was a sobering experience. Something that really struck me about the place was the logistics involved in delivering and killing 12,000 men, women and children on a daily basis. The camp was a machine designed for the purpose of extermination. Its always important to bear in mind where science and engineering can be directed. Too often I think the Nazis are portrayed as raving madmen, whereas in reality the people who designed Auschwitz were not stupid or insane, and probably not so unlike me and my colleagues.

Beam Profiling at NTOF

Using a silicon medipix to align the Neutron beam at NTOF, a time of flight facility at CERN.

MMND 2014

Off to Australia to the MMND (Micro, mini and nano dosimetry conference) in Port Douglas, Queensland. I took the opperturnity to see some crocodiles, travel up the coast and go snorkelling on the Great Barrier Reef on the social day (the conference had a social day! This should be more common!). I also gave a presentation on the results obtained during my time in Houston.

Wollongong

Back in Wollongong, just a few photos of the New South Wales coast.

Playing with SDD's

Playing with a silicon drift detector we found lying around. Seems to work reasonably well (picture is a pulse height spectra of Iron 55).

Repairing Christmas Lights

Attempting to repair an old set of Christmas lights. I think the capacitor needs replacing...

Success!

Iceland

We spent a week in Iceland over the Christmas break. It is a really spectacular place and we also got to see the Northern Lights. It would be quite fun to see what a Timepix would measure in the stratosphere during an aurora.

Snow on the Jura

Went up Le Reculet in the Jura mountains today. At Le Tiocan the snow was already several feet deep and became pretty much impassible above this (even with snow shoes).

More Snow

More snow for St Genis. Snow isn't terribly common in the UK and its arrival normally meant a day off school if your a child (and getting stuck in traffic otherwise) - still makes me happy if there is a lot of it.

Fondue in California

Off to California for a family wedding. Naturally I gave them a fondue set and a Swiss friend supplied some authentic mountain cheese. Because its in California they had to cut up carrots to go along with the break. Said Swiss friend was 'shocked and appalled'. Professionally I am starting to write my thesis.

Still Writing

Here is a pretty photo of Geneva.

Even more Writing

Now its springtime outside. The sun is shining!

Beamtime at CERF

Went to the CERF facility at CERN today for beamtime and did test microdosimetry measurements with the Gempix. No photos this time unfortunately.

Playing with TikZ

TikZ is a framework for producing formal diagrams in LaTeX. Seems to work pretty nicely.

As seen in Singapore Airport

Singapore also has a butterfly garden, a small food court that does fairly representative hawker food, a cinema and the worlds largest airport slide (I didn't know that this was considered competitive).

Measurements at the Calibration Lab

Did some measurements with our prototype timepix based neutron dosimiter at the CERN Calibration lab today.

Timepix measurements with Heavy Ions

In early January we were able to run parasitically on the H8 beamline.

We took several different measurments of a mixed heavy ion field with an average A/Z of 2.0 and 2.5. Some example tracks are shown below.

And a photo of the setup (with the Houston Medipix group and some CERN medipix chips as well)

Timepix measurements with Protons

In February we took data using timepix chips at a proton cyclotron in Bern

The main aim of the measurements was radiation hardness testing of the timepix chips with silicon sensors and naked timepix chips

Outreach in Sheffield, UK

In March I spent 2 days in Sheffield, UK leading outreach for the universities Dream Bigger Dreams campaign (aimed at bringing disadvantaged children into university).

I ran six sessions with children on hot, cold and liquid nitrogen (I blew stuff up for two days!).

Clustering with MAfalda

I have recently been using the MAfalda framework (link) to work with my Timepix data. MAfalda is a framework build on top of root that simplifies the process analyzing Timepix data. It has a number of cool features, not least those offered by Root (serialization, intelligent file IO, trees and decent plotting features). With a bit of hacking around it possible to do some pretty cool stuff. For example below I am running a clustering algorithm and pushing the different clusters into different windows for an online look at the data.

EU Commisioner Visit To CERN

Last week Androulla Vassiliou, European Commissioner for Education, Culture, Multilingualism and Youth visited CERN. As part of this visit a poster session was organized where all of the Marie Curie programs at CERN were presented.

Brewing!

Last weekend I made a trip back to the UK to see some old friends. While I was there we seriously upgraded Chris beermaking setup with proper plumbing, a DIY electric boiler, a new pump system and a PID temperature controller. The next step is clearly a series of sensors and a ROOT interface. Warning, dubious electrical safety ahead...

New Lab!

After several months the lab next door is finally complete!

Timepix Wafers

I saw a Timepix wafer today at a clean room at CERN, fresh from fabrication at IBM. I also learned a fun (...) fact, Timepix chips are typically named something like I04, F10, and similar. This refers to their physical position (column and row) on the wafer.

ARDENT Visit to CERN

The ARDENT ESRs came to CERN today for a meeting. As part of this I arranged a trip down to the ATLAS cavern to see the detector.

Flat White Success!

We have had a Gaggia Unica super-automatic coffee machine in the office for a few months now. It makes a reasonably nice espresso (miles ahead of the CERN cafeteria at any rate) but steaming decent milk on it for a nice Flat White (a short, strong milky Australian confection) in the morning has always eluded me. Turns out the trick is to remove the little plastic widget at the end of the steam wand, suddenly I could make pretty good foamed milk (as opposed to the gloppy froth from before).

Pretty Graphs in ROOT

ROOT can make some very pretty graphs if you play with it (these ones are of spins states in a hexagonal Ising model).

Holidays and Neutrons

I spent a few weeks this month on holiday moving around Europe, in total we hit six countries, drank some good coffees (I can tick the Greek Frappe and Neopolitian espresso off the hit list) and generally loafed around. I also took some measurements with a Timepix and a neutron source at the end of the month when I got back to CERN.

Upcoming Secondment in Wollongong

I will starting a 2 month secondment at the University of Wollongong this month. While there I will work on Geant4 simulations of the Timepix system (specifically for neutron detection).

Work and play in Wollongong

Some pictures of Wollongong, including some measurements with a Timepix taken at a photon linac.

Even after a year, Timepix can still surprise me

Before calibration the Timepix can be a little tricky. For example shown below is the TOT spectrum of an Americium source. Notice that there are three peaks in the uncalibrated spectrum but only two when calibrated.

If we break the spectrum up into where the hits came from, the origin of the third peak becomes visible. Its from two pixel hits before they are calibrated. Its obvious when I think about it, but it shows how even a simple energy calibration can improve your data.

Shell Scripting...

Terrible puns abound in computer science. At least I know regular expressions now...

Tea!

As a proper Englishman I drink it builders strength with milk in a mug that declares my allegiance to salty yeast based spreads.

What a coincidence!

I spent a few hours this afternoon playing with the external triggering electronics on the FITPix box with some colleagues in Wollongong. The idea was to get both detectors triggering in conincidence. Seems to work pretty well.

Return to CERN and the Open Days

I am now back at CERN for the open days (which I spent Saturday afternoon volunteering for). I got a great view of Mt Blanc (a common occurrence when approaching Geneva Airport from the south it has to be said) on the way over.

Second ARDENT workshop

Went to the second ARDENT workshop at the Politechnico di Milano. We ran an outreach event on various radiation detectors with local schoolchildren which was a lot of fun. I also gave a talk on my research. Milan isn't the most interesting city from a tourism point of view, but it does have an abundance of nice restaurants and is a lot of fun.

IEEE NSS MIC Conference

Off to the IEEE NSS MIC conference (where I have a presentation) in Seoul, Korea. Korea is a fantastic town with an abundance of good food (if you like Kimchee anyway). I also went to a cat cafe which was a novel experience.

As seen at Geneva Airport

Proton Therapy Measurements in Trento

Off to a proton therapy facility in Trento, Italy for measurements with EURADOS. Trento is a really pretty town in the Dolomites, it has quite a unique mix of German and Italian culture - think huge great beer halls serving pizza and pasta.

Medipix Measurements at Legnaro National Lab

Testing some different converters at a neutron beam at INFN Legnaro. INFN Legnaro is quite a nice little place that always seems to be perpetually foggy. Also the cafeteria is fantastic...

Holiday Travels

Time for some holidays. We hit Dubai, Bangkok, Phuket, Chiang Mai and Hong Kong.

More tests at Legnaro

Back to INFN Legnaro for more tests.

CERN in the Evening

Beam Time at CNAO

Off to CNAO to test the Gempix (a new detector with a CMOS ASIC to readout a gas electron multiplier) for beam monitoring. CNAO is a hadron therapy facility in Pavia, Italy. They have a synchrotron so they can deliver both carbon and proton ion beams.

Clean Lab

A clean lab is a happy lab... Or something.

Back to Wollongong

Back to Wollongong for two weeks. Here is something new, multilayer plastic converters 3D printed for the medipix, the idea with these is that they mimic some response function when you integrate over the whole chip. Time to see if they work.

Back to CNAO

Back to CNAO. Turns out the restaurant next to the hotel we stay in in town is quite good. These things matter after you've spent 16 hours in a small room underground.

English Breakfast

I've you've ever wondered what a full english breakfast should look like, the answer is this (taken at Fagins in Sheffield).

60th Anniversary Open Days

Open days at CERN. We had a stall on medipix at CMS (shown below is Alvin explaining the wonders of the universe). As part of this I finally did the CMS tour. CMS is a smaller detector than ATLAS but in a similar sized cavern. Because of this you can walk around the detector and get a more comprehensive view of it. I have to say that it is much prettier than ATLAS.

Parking

As seen outside restaurant 2. No comment.

Back to CNAO - Never Blindly Trust GPS...

Never trust GPS. The one built into our rental though that this road was preferable to the Autoroute. It wasn't. The rest of the beamtime was a success.

Quad Timepix ASIC

Here is something fun, a naked quad timepix ASIC. Normally these are covered in a seamless silicon sensor so you can't see the gaps (although the pixels at the border are bigger so they count higher), but for the Gempix we don't need a sensor.

Vulcan Bomber

As seen at London Southend Airport while travelling through. This one is apparently the only airworthy specimen.

Geneva

Geneva is a very photogenic city, especially on a sunny, summers day.

Off to Texas

Off to an extended secondment with the University of Houston and the NASA space radiation analysis group. NASA have six Timepix units on the International Space Station that they use to do charged particle dosimetry.

Rockets

Of course there are rockets at Johnson Space Center in Houston. Lots of rockets.

Mission Control

Mission control and the radiation console at NASA JSC.

Apollo Mission Control

Apparently these are the original machines from back in the day. Seeing this stuff was amazing, I grew up on a diet of rockets and moon landings. Covered in an assortment of buttons these are obviously not computers in the way I am used to thinking about them. That these took men to the moon and back is amazing.

WORMISS in Krakow

Off to give a talk at WORMISS (Workshop on Radiation Monitoring on the International Space Station) in Krakow, Poland. This is the second time I’ve been to Krakow, and its been just as fun as the first.

Auschwitz

I took the opportunity to visit Auschwitz which was a sobering experience. Something that really struck me about the place was the logistics involved in delivering and killing 12,000 men, women and children on a daily basis. The camp was a machine designed for the purpose of extermination. Its always important to bear in mind where science and engineering can be directed. Too often I think the Nazis are portrayed as raving madmen, whereas in reality the people who designed Auschwitz were not stupid or insane, and probably not so unlike me and my colleagues.

Beam Profiling at NTOF

Using a silicon medipix to align the Neutron beam at NTOF, a time of flight facility at CERN.

MMND 2014

Off to Australia to the MMND (Micro, mini and nano dosimetry conference) in Port Douglas, Queensland. I took the opperturnity to see some crocodiles, travel up the coast and go snorkelling on the Great Barrier Reef on the social day (the conference had a social day! This should be more common!). I also gave a presentation on the results obtained during my time in Houston.

Wollongong

Back in Wollongong, just a few photos of the New South Wales coast.

Playing with SDD's

Playing with a silicon drift detector we found lying around. Seems to work reasonably well (picture is a pulse height spectra of Iron 55).

Repairing Christmas Lights

Attempting to repair an old set of Christmas lights. I think the capacitor needs replacing...

Success!

Iceland

We spent a week in Iceland over the Christmas break. It is a really spectacular place and we also got to see the Northern Lights. It would be quite fun to see what a Timepix would measure in the stratosphere during an aurora.

Snow on the Jura

Went up Le Reculet in the Jura mountains today. At Le Tiocan the snow was already several feet deep and became pretty much impassible above this (even with snow shoes).

More Snow

More snow for St Genis. Snow isn't terribly common in the UK and its arrival normally meant a day off school if your a child (and getting stuck in traffic otherwise) - still makes me happy if there is a lot of it.

Fondue in California

Off to California for a family wedding. Naturally I gave them a fondue set and a Swiss friend supplied some authentic mountain cheese. Because its in California they had to cut up carrots to go along with the break. Said Swiss friend was 'shocked and appalled'. Professionally I am starting to write my thesis.

Still Writing

Here is a pretty photo of Geneva.

Even more Writing

Now its springtime outside. The sun is shining!

Beamtime at CERF

Went to the CERF facility at CERN today for beamtime and did test microdosimetry measurements with the Gempix. No photos this time unfortunately.

Playing with TikZ

TikZ is a framework for producing formal diagrams in LaTeX. Seems to work pretty nicely.

As seen in Singapore Airport

Singapore also has a butterfly garden, a small food court that does fairly representative hawker food, a cinema and the worlds largest airport slide (I didn't know that this was considered competitive).

Measurements at the Calibration Lab

Did some measurements with our prototype timepix based neutron dosimiter at the CERN Calibration lab today.