Free ImageJ Macro -- for citing images

(of course all IJ macros and IJ itself are free...)

So I got sick of constantly clicking away just to resize an image and add some citation text to the bottom and then name the file that exact thing; in fact, it was a deterrent to blogging -- yes, I am *that* lazy, apparently. At 4 in the morning today, my latent inner yet-unexplored codemonkey decided it needed an ImageJ macro for doing that, and it needed it then, at 4 in the morning, the day before I fly for holidays, and therefore a very busy day. After a couple hours of failed negotiation attempts between brick walls and my head (and much profanity), I finally produced a piece of code that not only does something, but does what I want it to! Being an utter failure at anything technical (engineering aptitude turns out to not be particularly heritable, as my parents' experiment demonstrates), I get soooo excited when something I slap together out of copy+paste and single-finger typing on the keyboard actually works, that I absolutely have to share it with the world. Even if it's pathetically minor and useless. Shhh.

World, behold -- an ImageJ macro for adding citations to images!

// This macro creates citation (or other input) text by adding a 20p strip to the bottom of the image, aligned right

// Image is saved in Documents as the ref input text

// WARNING: saving several images with same citation input WILL result in overwrite!

ref=getString("Reference", "ref");

var width = getWidth();

var height = getHeight();

height=height+20;

run("Canvas Size...","width=&width height=&height position=Top-Center");

var textwidth=getStringWidth(ref);

var textmargin=width-(textwidth+5);

drawString(ref,textmargin, height-5);

var path="C:\\";

var name=path+" "+ref;

saveAs("Jpeg",name);

Hopefully this means I'll get back to regular blogging soon, as one more Gate of Laziness has been removed from the path. Now if only IJ could also upload and link those images...

Why I did not blog this weekend...

Happy New Year, everyone! (hey, it's still January...) While I did only get back a week ago, with plenty of urgent offline matters to attend to, I was totally going to dust off the blog this past weekend. But I didn't. As much as I enjoy protists and writing for you, I just had to take the liberty to sneak off from the internet and enjoy THIS:

That's right, I actually went outside and explored those pointy things outside my lab window up close and personal. (have I mentioned being able to see snow-capped mountains from the lab pretty much year-round, except for maybe late August-early September? ;p) Tried out backcountry skiing (telemark) for the first time, though that didn't work out too well due to a combination of an impressive sheet of ice, steepness, busy trail with ruts and holes everywhere and bindings that didn't want to fit properly...so the skis were mostly carried. Uphill and downhill. Ah well, will actually check snow conditions next time (some seasoned skiers also resorted to carrying them so we didn't feel so bad).

Went with a pretty large group (university-affiliated), the point was actually winter camping. In snow caves. Igloos too, but those are freaking impossible to build, it turns out. If Canadians really did all live in igloos, we'd all be structural engineering geniuses up here. My friend and I resorted to a simple cave to start with:

Yes, you really do wake up to that shade of blue. Does the ceiling look thin? There's a good half a metre of snow up there. Amazing how much light it lets in. It had pretty good insulating properties, kept things warm - at around 0˚C. The other option was -12-15˚C outside...oh yes it was freaking cold. Meanwhile, in the distance lay the city with it's non-freezing temperatures and sane people who got to sleep without worrying about hypothermia and frostbite. Without their hair freezing to snowy walls even!

Sure they had the warmth and luxurious comfort, but did they have this to surround them when they woke up?

Did they get harassed by these rather bold birds as they tried to eat breakfast? Seriously, that little grey bird (apparently a jay) would approach you to about 20cm away and not care. Even the ravens were a little more cautious...

And where there is ice, there are ice sculptures. Natural or man-made. (neither of them are mine)

One of the wonderful things about camping is that you get a rush of euphoria from the simplest things. Like hot tea. Or getting home with all your toes still intact. Somehow, those things become much harder to appreciate back in the city.

Apologies for total off-topic-ness and protist-less-ness (was going to sample but it was waaay too cold), but it's kinda fun to step back and look at a different scale from time to time, especially for a microscopist. And I'm ashamed for not having taken much advantage at all of living in such a beautiful place. Anyway, protist blogging shall return later, after I get back from ScienceOnline 2011, which should be after the 19th. Also, there may or may not be some exciting announcements to make. Watch this space...

Scaled protists and bloated distractions

Ok, I was gonna just post this picture as filler, and then suddenly got sucked into the microbial biogeography debate – you know, "is everything everywhere?" etc. So I was going to write up a quick blurb on that, but it somehow grew out of control. As I don't have time for such epic digressions at this moment, esp w a promised post quite overdue, amidst other stuff, I'll just shelve that for later and simply post the pretty picture instead. Enjoy this lineup of protists scaled to the size of a pinhead:

How many protists can dance atop a pin? (Finlay 2002 Science)
I'm going to try to vaguely identify them, from left to right: Chaos sp.; Stentor sp.; some random amoebozoan; Amoeba sp.; Loxodes? man I suck at this; Bursaria sp.?; Paramecium sp.; Mayorella sp.?; a euglyphid; another bloody ciliate; Strombidium; Difflugia-like thing; Euplotes; Ophryscolex-like; heterotrophic euglenid; heterotrophic euglenid again (Peranema); het eugl (Entosiphon or Petalomonas), Chlamydomonas? too small; ?, pedinellid-like thing?; Bodo, non-descript small unknown flagellate? Bodo., last two look like those tiny non-photosynthetic stramenopiles everyone ignores.

This tangent was initiated by working on that long overdue post, by the way. Apparently, one graph is enough to lead me on a massive multi-window-tab-explosion journey into the wild unknowns, even if it involves ecology. Maybe this is why it's taking me like four months to write a single freaking chapter. I'm not sure the free version of Mendeley was meant to handle hundreds upon hundreds of references. Let's see what it does once I hit a thousand, which will be soon. At least researching flagellar root apparatuses doesn't typically lead me to Hooke's description of the first cell, unlike one particular reader here =P (who needs to update, by the way...)

Oh, and submit to the carnivals! The more posts I have, the lest posts I'd have to fake, and the less I must rickroll you with fake links...

Snippets of the beauty of sliced axonemes

Look what I found in obscure ultrastructure literature!

It's a star! (Ringo 1967 J Cell Biol)

That's a cross section through the transitional zone of the Chlamydomonas flagellum. The geometric intricacy actually comes from the need to transition from nine triplets of the basal body to the flagellum's nine doublets and a central pair (of microtubules). As evident in the figure below, this can get quite tricky:

Cross-sections through a Chlamydomonas flagellum and basal body. (Ringo 1967 J Cell Biol)

This could be inspiration to some fun baking project...

Speaking of sliced flagella, there are some more wonderful patterns hidden away in the axonemes of rather obscure 'heliozoans' (centrohelids and actinophryids):

Left: Spiral arrangement of microtubules in the axoneme of actinophryid(?) Echinosphaerium. (Jones & Taylor 1981 JCS) Right: Cross section through an axopod of Actionosphaerum (actinoprhyid) containing an axoneme in the centre. m - mitochondrion. (Tilney et al. 1961 JCB)

(axonemes are the cytoskeletal support within axopodia, the long spikey protrusions that make the creatures appear like miniature suns)

And here's one so bizarre it takes three additional diagrams to explain it:

Axoneme of Cienkowskya mereschkovskyi*, a centrohelid 'heliozoan' reportedly closely related to Heterophrys. (Febvre-Chevalier + Febvre 1984 Origins of Life)

*To the slavic ear, this sounds painfully like a masculine adjective applied to a feminine genus name...owww.

And back to basal bodies, parabasalian TEMs are a work of art in their own right. Especially from Joeniids:

Rows of basal bodies in the ciliary region of Pachyjoenia howa. (Brugerolle & Bordereau 2004 Eur J Protistol)

This has nothing to do whatsoever with neither protists nor axonemes, but rather a funky-looking reject from my research images. It's cytoplasmic GFP in a partly lysed plant cell (normally the GFP should look diffuse) Not sure why it does that though, but often lysing cells become very bright, and squashed material is lush with autofluorescence.

My favourite colour is GFP.

Real posts to come soon... still mildly overwhelmed by stuff at the moment. Currently working on gathering up literature both new and old on a supergroup that may or may not actually exist, and is a complete and total mess either way (the new 'Hacrobia'). On top of other things.

To give you an idea, the previously incertae sedis centrohelids are in it, apparently, and their older grouping, "heliozoa", has only recently been dissolved (Nikolaev et al 2004 PNAS), so what is now spread out over at least two supergroups (centrohelids in 'Hacrobia' and actinophryids in Stramenopila) used to be lumped under one category and now you might as well rip all your hair out trying to figure anything out in there. It basically means you have to deal with the damn things on a genus-by-genus, taxon-by-taxon basis. (luckily, they're really cute so it's not that bad ^^) Also, a couple extensive papers happen to be written by The One We Fear, and I'm still denying the fact I may eventually have to actually read them. Grrr. Oh, and add to that the horrible and sometimes altogether lacking availability of older literature, requiring you to assemble epic shopping lists for the inter-library loan people...

Should probably also write another sentence of that manuscript to feel as if I've done something this week. Describe a couple more figures that don't actually exist yet... wish all my control pictures didn't totally suck. Redoing experiments again to get better images of...controls. Sigh. Working on projects in two completely unrelated fields (and different buildings) is a bit draining... /rant

Do giant deep sea isopods have protist endosymbionts?

Apparently not as of this [admittedly slim] description of intestinal microbes from 1982. Seems to be mostly bacteria and nematodes - though one wonders if there are some cool gregarine or something inside one of those.

On the topic of isopod gut endosymbionts (though not of the deep sea), there's a recent PNAS paper starring a wood-boring isopod devoid of cellulose-digesting gut microbes, capable of lignocellulose digestion all on its own! (King et al. 2010 PNAS "Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes") Limnoria quadripunctata, quite amazingly, actually lacks gut microbiota entirely (unlike the bivalve woodboring 'shipworms', which do have a flourishing gut culture) and as animals are known for failing at lignocellulose digestion on their own, raised some interesting questions about how they do it.

Turns out, Limnoria not only has unusually high glycosyl hydrolase (GH) expression levels in its transcriptome, but also the first described case of endogenously produced GH7 in metazoa. This was then followed up by finding GH7 expression in the Daphnia and Gammarus(both also crustacea) ESTs. Seems like the GH7 domain is key to self-sufficient cellulose digestion, in animals anyway. Another question is...how did it get there? LGT from somewhere? The authors consider recent LGT unlikely as the metazoan sequences are quite distant from anything else in tree (and don't fall in the midst of another clade; though there's arguably too few sequences to judge at this point).

Thus, it seems that what most strikingly enables the gastromicrobially deprived Limnoria to digest wood on their own is GH7 (and potentially hemocyanins). Curiously, the most abundant cellulases in the termite gut, produced mostly by its protist symbionts, are GH7.

This little adventure, like most others on this blog, was completely unplanned and sporadic. Someone brought up deep sea isopods, thus I couldn't just ignore that very important question of ultra high priority. Mostly because giant isopods are fucking cool. Oh, and giant. Would make an adorable, wonderful pet, if it weren't for the whole deep sea thing.

Source: Ross Gwynn on Reddit. 2.5 feet long, or roughly 75cm, though that may be exaggerated.

Assorted links: Protaxites, ciliate sex and publication tweets

Still procrastinating with Sunday Protist, which means I'm actually procrastinating with all the real work I should be doing right now...but here's some random stuff my internet wanderings have taken me to!

Giant columnar fungi(Protaxites) may have actually just been rolled mats of liverworts -- Catalogue of Organisms. Intriguing indeed!

Really nice article on ciliate sex by Olivia Judson. When I first read her dino article earlier, I was like "holy crap a science writer actually got the facts straight! o_O" And then I noticed she's a practicing biologist -- never mind the 'writer gets facts straight' headline. On the other hand, 'scientist can actually write' is in itself quite an impressive headline, so it's no less amazing!

#sci140: A paper in 140 characters (new publishing model). A bunch of geeks decide it's about time to put Twitter to good use -- can you summarise a classic paper (or your own) in 133 characters or less? (7 letters go to the hashtag)

Some of my favourites:

• SelectAgent #sci140 Salt of DNA structure= double helix. Strands anti-parallel; has implications. (PS Rosie didn't help)
• michaelgrr We did some messing about with wire and stuff, found double helix fits the Xray patterns of DNA. Rest is obvious. Suck that, Linus! #sci140
• IanMulvany #sci140 dog + bell + food = saliva. Repeat. Eventually dog + bell = saliva, where's my nobel prize?
• labgrrl Oops, Who would've thought that absolute power corrupts absolutely? (Zimbardo,1971) #sci140
• sciencebase: Dropped heavy and light ball at Pisa; saw landed at same time. Peer review problems now, especially after telescope incident. #sci140
• pssalgado cat in box + decay triggered poison. box closed: cat alive & dead. when box opened: cat live or dead #Schrodinger #sci140
• michiexile #sci140 Complete. Concise. Consistent. Pick two. - Gödel 1931
• aeporreca It’s impossible to determine whether a guy with an infinite piece of paper will ever stop doing maths. http://bit.ly/9qKV5E #sci140
• bparsia All your theorems are belong to us (Euclid, 300BC) #sci140
• axiomsofchoice p,q∈ℕ;p²=2q²⊧p∈2ℤ;gcd(p,q)=1⊧q∈2ℤ+1;∵4∣a²,a∈2ℤ⊧q∈2ℤ⊧⊥;∴√2∉ℚ;QED #sci140 http://ff.im/fFJeG
  

Btw, it's a competition. Get crackin'! (I don't have Twitter so I'll just watch...)

Awesome flash game: Microbe Combat

http://www.flashraiders.com/242-Microbe-Combat.html

All we need is to make it more realistic, add bacteria (I hope the author(s) realise bacteria don't phagocytose, proving those microbes to be eukaryotic...they do seem to have nuclei though), add a few more organisms like amoebae, flagellates, a Hypermastigote or three, and...PARASITES! =D and we have a whole new genre of gameplay!

This could be so pretty! And sexy, since we're talking about eukaryotes. Any programers out there? *drools*

Anyway, must go back to play some more get real work done.

Assorted link roundup

Some links from my epic procrastination foray:

Since I'm supposed to be cramming studying for my developmental biol lab exam (early chick embryology) this Monday (8am, ewww), NOVA's Guess the Embryo was quite fun! And amazingly difficult too... (the bat develops quite cutely, for some reason.)

An interesting application of DNA barcoding: testing sushi meat

Science standup comedy, via MolBio. On that note, lab cartoons, also via MolBio.

Forgot where I found this (was quite a while ago), but How to write consistently boring scientific literature (Sand-Jensen 2007 Oikos; free access) has 10 simple rules to ensure your scientific work never falls into the hands (or mind) of others.

CG animation of Aspergillus conidiophores via MycoRant. Fungal fruiting bodies seem very graceful there!

10 days left for 2009 Open Lab submissions, due 01 December at midnight.

And I guess that's it for now. Should probably get back to drawing embryos over and over and over again. Also, why is mammalian developmental biology literature so bloody hard to read? Plant people are kind enough to provide sufficient background for everyone, even zoologists, to understand what's going on. The mammalian guys assume you know everything already. Hello, some of us actually work with different systems, y'know?

It's kinda fun to be thrown in at the deep end of a completely foreign field though. Too bad we're expected to focus on only one paper for the class presentation thing, and I like to skim over a small pile of reviews before narrowing in on one topic. That seems to be quite discouraged, considering the time alotted to this endeavour. Maybe that's why I seem to get along quite well with TC-S papers (aka Megamonumental Reviews of Life, the Universe and Everything). FUZZBRAIN PRIDE!

When I take over the world, undegrad is going to be run so differently. Also, microbiology and protistology would be the most well-funded fields. Disciplinary tribalism will be banned, and everyone will work together and learn from each other's fields, even arts and science. Engineers will be banished to a deserted island in the middle of the Pacific somewhere. The steady state for a sane social model will be found, and societies will be engineered towards it, somehow. (all previously invented utopias failed to be steady states; this one will be different. Mwahaha) LOLcats will be displayed proudly and ceilingcat will be worshipped on Caturdays, along with FSM and various protist and bacterial demi-gods. And there will be NO bloody sweet meat. Evar. Sweet meat is a freaking abomination - how the HELL can anyone in their right mind pour honey over a delicious beef steak? That's just horrible. A crime against culinary arts, a grotesque malfunction of the human culinome. Seriously, new -ome coinages cannot begin to compare with the abomination that is sweetened meat*.

*Exceptions include: apples and cranberries in duck, turkey et al. And NOTHING ELSE!

And finally, the theft of forceps from microscopists will be a capital offense. I NEED THOSE FORCEPS FOR MY WORK, YOU %$@&$s.

I think I'm ready to quit procrastinating for a while...

Rule 34: Proteins

(alpha-helix, beta-barrel)
The reader is now encouraged to go out and find real examples of protein Rule 34 in action. There must be some suggestive protein interactions out there somewhere! And we shall never view biochem the same way again...

Inspired by this comment...


PS: In light of Jonathan Eisen's 'competition', shall we hereby coin 'pornome'?

How about genomeome, a set of genomes? "The genomeome of this phylum suggests..."
And then genomeomeome "A comparative analysis of genomeomes in multiple phyla led to the assembly of a larger genomeomeome..." I can keep going. But now we're getting off-topic...

Homage to RefWorks...

I wish Blogger had RefWorks citing capabilities... I've gotten spoiled by clicking the 'cite' button to cite stuff. Here I actually have to write out the full citations. By hand. The horror.

Luckily, I can preformat stuff there and just copy it over here. Blogging has just got a ton easier.

Sadder than my newfound dependency on citation managers is that I actually think they're like the coolest thing ever. There was actually a rush of euphoria when I discovered cursing the process of typing bibliographies is a thing of the past! I even investigated all the various citation styles and...yes, found my favourite one.

I have a favourite citation style: of the Current Opinion series. I even have a rationale for liking it. Look how neat and easy to follow it is:

Cavalier-Smith T: Predation and eukaryote cell origins: A coevolutionary perspective. The International Journal of Biochemistry & Cell Biology 2009, 41: 307-322.

The bold formatting option exists to be used, either for the author or the title. The author is usually first anyway, so it makes more sense to bold the title. The numbered in-text citations [1] make it easy to follow review papers without the clutter of full in-text references. (although the full format comes in handy at time too...) The only issue I have is the year appearing at the end. I prefer the pub year to appear right after the author, since in biology it's fairly important to know when stuff was said/done. I hate that about the wretched MLA: they don't even use year in their in-text refs!

I randomly blogged about citation styles.

I think I've just reached the epitome of geekdom. To beat that, you must argue for YOUR favourite citation style.

However, in this post is a preview of paper I will be working on translating into English for you guys, from the TC-S dialect of academese... it's on the evolution of eukaryotes from prokaryotes. Fascinating stuff!

Now I'm actually gonna do it...

I've been studying...

Thought you guys needed proof:

And then we ditched our beer cans on an unsuspecting lab's drink shelf (that's what it's really for, right? The fine art of beer arrangement?) Mwahaha, who'd like to be the next victim?

(PI's name blurred out since I doubt they'd like to be associated with the likes of us... <_< )


No really,


That's about a third of the organisms we need to know for tomorrow's exam. Their life stages/cell structure/special features too. Ignore the arrangement of non-photosynthetic heterokont phyla -- they're randomly placed. Also, I insist on calling the Cryptomonad/Haptophyte clade 'Crhaptophytes' even though it got rejected. Actual protistologists, please assist this noble cause by using that wonderful taxonomic term proliferously! Thanks.

To cite aforementioned phylogenetic mess, please use (Wavefunction, P. 2009, SkepticWonder). Methods consist of: Chalk, modest volume of EtOH, exam panic. References: More people who would not like to be associated with the likes of us XP

Hmmm... I haven't stated anything utterly controversial on this blog yet. Here we go:

"Cell biologists are superior to molecular phylogeneticists."

(Cue 'real' botanists: "Arabidopsis is NOT a plant!!!1!!one!!!")

Let the wars begin! *cracks open another can of beer and sits down to watch*
*evil laughter*

Ok I'll stop embarassing myself with pointless rambling... I overstudied. TOKOPHRYA!!! BLEPHARISMA! TETRASELMIS! CHILOMASTIX! ACHLYA! VAUCHERIA! NOCTILUCA! CRICOSPHAERA! EIMERIA! CYANOPHORA! ...can't stop...feel bad about ignoring groups... aaaaahhhh.... (we didn't have time to cover Rhizarians though *weeps* )

Thought of the day

I wish I worked on Zea mays (corn)... so that upon saying "I'd rather watch grass grow", I would actually be serious...

That's it. Did you expect something profound?

(Busy days yet again...)



Addendum: Now if I were a chemist in the paint industry... ah, possibilities... =P