Adventures in Code III: the quantixed ImageJ Update site

We have some macros for ImageJ/FIJI for making figures and blind analysis which could be useful to others.

I made an ImageJ Update Site so that the latest versions can be pushed out to the people in the lab, but this also gives the opportunity to share our code with the world. Feel free to add the quantixed ImageJ update site to your ImageJ or FIJI installation. Details of how to do that are here.

The code is maintained in this GitHub repo, which has a walkthrough for figure-making in the README. So, if you’d like to make figures the quantixed way, adding ROIs and zooms, then feel free to give this code a try. Please raise any issues there or get in touch some other way.

Disclaimer: this code is under development. I offer no guarantees to its usefulness. I am not responsible for data loss or injury that may result from its use!

Update @ 10:35 2016-12-20 I should point out that other projects already exist to make figures (MagicMontage, FigureJScientiFig). These projects are fine but they didn’t do what I wanted, so I made my own.

Come To California

I’ve returned from the American Society for Cell Biology 2016 meeting in San Francisco. Despite being a cell biologist and people from my lab attending this meeting numerous times, this was my first ASCB meeting.


The conference was amazing, so much excellent science and so many opportunities to meet up with people. For the areas that I work in: mitosis, cytoskeleton and membrane traffic, the meeting was pretty much made for me. Often there were two or more sessions I could have attended, but couldn’t. I’ll try to summarise some of my highlights.

One of the best talks I saw was from Dick McIntosh, who is a legend of cell biology and is still making outstanding contributions. He showed some new tomography data of growing microtubules in a number of systems which suggest that microtubules have curved protofilaments as they grow. This is in agreement with structural data and some models of MT growth, but not with many other schematic diagrams.

The “bottom-up cell biology” subgroup was one of the first I attended. Organised by Dan Fletcher and Matt Good, the theme was reconstitution of biological systems in vitro. The mix of speakers was great, with Thomas Surrey and Marileen Dogterom giving great talks on microtubule systems, and Jim Hurley and Patricia Bassereau representing membrane curvature reconstitution. Physical principles and quantitative approaches were a strong theme here and throughout the meeting, which reflects where cell biology is at right now.


I took part in a subgroup on preprints organised by Prachee Avasthi and Jessica Polka. I will try to write a separate post about this soon. This was a fun session that was also a chance to meet up with many people I had only met virtually. There was a lot of excitement about preprints at the meeting and it seemed like many attendees were aware of preprinting. I guess this is not too surprising since the ASCB have been involved with the Accelerating Science and Publishing in Biology (ASAPbio) group since the start.

Of the super huge talks I saw in the big room, the Cellular Communities session really stood out. Bonnie Bassler and Jurgen Knoblich gave fantastic talks on bacterial quorum sensing and “minibrains” respectively. The Porter Lecture, given by Eva Nogales on microtubule structure was another highlight.

The poster sessions (which I heard were sprawling and indigestible) were actually my favourite part of the meeting. I saw mostly new work here and had the chance to talk to quite a few presenters. My lab took three posters of different projects at various stages of publication (Laura’s work preprinted/in revision project presented by me, Nick’s work soon to submit and Gabrielle’s work soon to write up) and so we were all happy to get some useful feedback on our work. We’ve had follow up emails and requests for collaboration which made the long trip worthwhile. We also had a mini lab reunion with Dan Booth one of my former students who was presenting his work on using 3D Correlative Light Electron Microscopy to examine chromosome structure.

For those that follow me on Twitter, you may know that I like to make playlists from my iTunes library when I visit another city. This was my first time back on the west coast since 2001. Here are ten tracks selected from my San Francisco, CA playlist:

10. California Über Alles – Dead Kennedys from Fresh Fruit For Rotting Vegetables

9. San Franciscan Nights – The Animals from Winds of Change

8. Who Needs the Peace Corps? – The Mothers of Invention from We’re Only In It For The Money

7. San Francisco – Brian Wilson and Van Dyke Parks from Orange Crate Art

6. Going to California – Led Zeppelin from IV

5. Fake Tales of San Francisco – Arctic Monkeys from Whatever People Say I Am, That’s What I’m Not

4. California Hills – Ty Segall from Emotional Mugger

3. The Portland Cement Factory at Monolith California – Cul de Sac from ECIM (OK Monolith is nearer to LA than SF but it’s a great instrumental track).

2. Come to California – Matthew Sweet from Blue Sky on Mars

1. Russian Hill – Jellyfish from Spilt Milk

Before the meeting, I went on a long walk around SF with the guys from the lab and we accidentally found ourselves on Russian Hill.


For some reason I have a higher than average number of bootlegs recorded in SF. Television (Old Waldorf 1978), Elliott Smith (Bottom of the Hill, 1998), Jellyfish (Warfield Theater 1993), My Bloody Valentine, Jimi Hendrix etc. etc.

The post title comes from #2 in my playlist