Andrew York @AndrewGYork Twitter profile

Pinned Tweet

Andrew York

7 years

Re-imagine scientific publishing. What would you change? My answer: No paywall, no delay, straight to the web. Open data, open code, interactive/animated figures. Transparent, rolling peer review, version control, CCBY license, citable DOIs. See it here:

48

430

1K

Last Seen Profiles

@Densurgeon46383

@NordMediaNW

@McrCommuter

@Its_thestorm

@CEO__Quest

@elisestephens

@noch_707

@alaanisnavarret

@psyg0th

@ms_sole_amazin

@koomahina

@cubeincubation

@ARCH1993

@SueGreenbergPR

@VforCheese

@SlovCG

@JoelSimonEP

@A3DGhost

@BigSteppertm

@EmiRingOfficial

@Giulidmr

@aklm_aklm568

@ANHS73

@joiningthefun

@SheraTheDJ

@uguisu_ume

@bwunni

@downtiMAK

@AshyTown_

@Summerxluvsu

@HarveLuiz88576

@rexypyp

@nicholaseberts

@RawMilkMamii

@naaktstrandje

@MaxFillsUrMom

Andrew York

@AndrewGYork

1 year

We discovered a surprisingly easy way to control the brightness of fluorescent proteins via magnetic fields: This raises fascinating scientific questions about the mechanism, and tantalizing technological opportunities for bioengineering.

55

350

1K

Andrew York

@AndrewGYork

3 months

Meet MagLOV: an engineered protein that responds STRONGLY to magnetic fields. This is a fluorescence timelapse of MagLOV in E. coli. We're waving a (small) magnet under the plate. Can you tell where the magnet is? Want some? It's on Addgene now!

45

322

1K

Andrew York

@AndrewGYork

5 years

Microscopy technique development's exploding, but core facilities still buy confocals. This ugly baby will end that. Less phototoxicity, WAY faster than confocal. NO DRAWBACK. Details here: Co-invented by @amsikking . Get one from jon @asiimaging .com

40

338

869

Andrew York

@AndrewGYork

3 years

Fluorescent biosensors reveal the dynamics of life, but *quantitative* biosensing only works in transparent single cells... until now! @Maria_Ingaramo figured out how to take robust quantitative measurements with fluorescent biosensors, in whole animals.

21

145

581

Andrew York

@AndrewGYork

5 years

I invented this technique. I'd appreciate acknowledgement and citation.

Evident Life Science

@Evident_LS

5 years

#WHITEPAPER : Learn the principles behind Olympus Super Resolution (OSR) technology and the optical design of the IXplore SpinSR system -

1

4

8

18

97

533

Andrew York

@AndrewGYork

5 years

Help us resolve a paradox, argue with Einstein, and make fluorescence microscopy a thousand times brighter. Ask your favorite physicist: "What direction does stimulated emission travel from a pointlike emitter?" Our answer: Co-inventor: @sanjay_r_varma

12

103

246

Andrew York

@AndrewGYork

5 years

Big update to our single-objective light-sheet project! Spoiler: now you can get a huge field-of-view. Don't like our reference design? Make your own! We've added a general recipe for producing your own custom version: (project driven by @amsikking )

8

59

242

Andrew York

@AndrewGYork

4 years

@acarriebear I'm amazed that our community is so insane that pirating our own output via a shady Russian website is effectively best practices. I wonder how many scientist-years of progress scihub is directly responsible for. A hundred? A thousand? Probably more.

0

15

228

Andrew York

@AndrewGYork

5 years

Behold the "Scandreas", a trivially-aligned light-efficient alternative to lens-galvo-lens scanning! Invented by Andreas Bodén @Bodeeen1 in @IlariaTesta4 's lab, with assistance from @andreavolpato_ (and me!) Video by @Kayley_Hake Cite this tweet:

13

49

225

Andrew York

@AndrewGYork

4 years

I'll probably be able to hire 1-2 inventors in the next year or so. For the right person, this is the best science job possible: intellectual freedom, stable/ample funding/salary, and a real chance at impact. Read the rest of this thread to learn why you SHOULDN'T apply...

8

78

225

Andrew York

@AndrewGYork

4 years

How do you share your microscopy data? How should I share mine? How do you use shared microscopy data? @coppola_s_PhD has an idea: let’s write an opinion piece together! @HenriquesLab and I are helping, and we need your help too! Read the rules here:

88

101

199

Andrew York

@AndrewGYork

7 years

Our second publication, an "open-source hardware" microscope add-on for blazing fast 3D imaging: Includes raw data, CAD files, parts list, build instructions, figure generation code, and example hardware control code. #OpenSource #OpenSourceHardware

9

62

170

Andrew York

@AndrewGYork

5 years

Another update to our single-objective light-sheet project: Proof-of-principle biological imaging! Courtesy of @UTSWNews superstars @RetoPaul , @kD3AN , @ErikWelf and Meghan Driscoll at UTSW. See the first-ever live snoutscope images here: CC @amsikking

4

27

165

Andrew York

@AndrewGYork

2 years

Mid-pandemic, I had a bizarre injury and lost the ability to walk for two months. Since then I've focused on recovery, celebrating and appreciating health. It's been >1 year and I'm still not fully recovered. I'm currently the strongest I've ever been, but also the most fragile.

8

0

166

Andrew York

@AndrewGYork

3 months

I hate when papers obscure protein sequences, so here's MagLOV in a tweet. MLATTLERIE KNFVITDPRL PDNPIIFASD SFLQLTEYSR EEILGRNpRF LQGPETDRAT VRKIRDAIDN QTEVTVQLIN YTKSGKKFWN LFHvQPMRDQ KGDVQYFIGV kLDGTEHVRD AAEREkVMLI KKTAENImEA AKEL (mutations vs AsLOV2 are in lowercase)

4

14

161

Andrew York

@AndrewGYork

4 years

@acarriebear I like your spirit, but this solution has second-order consequences: haves vs have-nots, each journal has monopoly to overcharge libraries, etc. Keeping any research behind a paywall is bizarre. Preprints are great, but maybe we should ransom pre-preprint research too.

2

1

151

Andrew York

@AndrewGYork

2 years

Hey biological image processing twitter: teach me a new skill! My climbing buddy @JenniferLangen has two types of images that are obviously different by eye. What's current best practice for quantifying "they're obviously different"? Relevant preprint:

49

21

145

Andrew York

@AndrewGYork

5 years

We want this microscope in YOUR hands, ASAP. Traditional publication takes years, commercialization even longer. Even preprints take time to prepare. Our fastest path is #OpenScience ; see for up-to-date parts list, build instructions, & preliminary data

2

28

118

Andrew York

@AndrewGYork

3 months

A nice surprise: @SjoerdStallinga cited my tweet :) Open discussion is the most productive form of scholarly publication. Smart people can tell good ideas even if they're not in fancy journals, and kind people give high-fives even when they don't have to. Thanks, Sjoerd!

Andrew York

@AndrewGYork

6 years

@SuperResoluSian @LennartHilbert @barrosolab Can you "coinflip split" the image? Meaning, scale image counts to photoelectrons, then flip a coin for each photoelectron to decide if it belongs in imaginary subexposure 1 or imaginary subexposure 2?

2

0

6

2

12

116

Andrew York

@AndrewGYork

5 years

Biologists Should Not Learn How to Read. When it comes to biologically relevant reading, we’re already starting to see the beginnings of publicly available text-to-speech (e.g., Alexa) that doesn’t really require much more than some very basic talking and knowing how to listen.

MiketheMadBiologistWhoLikeTrumpAlsoHasBoxes

@mikethemadbiol

5 years

Biologists Should Not Learn How to Code

50

25

135

3

10

114

Andrew York

@AndrewGYork

5 years

Inspired by several recent conversations, I'd like to clarify the following:

8

6

100

Andrew York

@AndrewGYork

5 years

I'm extremely happy with this response. This was very kind and considerate of @OlympusLifeSci , and means a lot to me. Thank you! And thank you to everyone for showing so much positive attention and support; I love the feeling that we're all on the same team.

Evident Life Science

@Evident_LS

5 years

@AndrewGYork Hi Andrew - As one of the researchers responsible for the super resolution methods that helped us develop the OSR algorithm, we updated our white paper to include proper citation. Thanks for bringing this to our attention; we appreciate your contributions to microscopy research.

1

27

1

3

98

Andrew York

@AndrewGYork

5 years

Fluorescence is the heart of countless technologies, but fluorescent measurements are often starved for photons. Fluorophores emit MUCH faster if they're "stimulated": So why don't we image via stimulated emission? Because it's impossible! ...or IS it?

7

26

90

Andrew York

@AndrewGYork

4 years

Imagine this situation without twitter. What venue would Dr. Bankhead have to tell his story? A letter in the journal a year later, if he's lucky? Who would read it? Say what you will about Science Twitter, it's an amazing venue for public accountability.

Pete Bankhead

@petebankhead

4 years

A small number of people know the real background story to @QuPath , but most don't. I didn't plan to ever tell it publicly, until a Google Alert today caught my eye. A thread about open science & academia 👇 (1/n)

38

294

847

2

7

89

Andrew York

@AndrewGYork

3 months

Imagine drugs that ONLY work near a magnet. Imagine eliminating drug side effects outside the target organ. Today, it's just magnetofluorescence, but we're working towards *magnetogenetics*: the ability to turn arbitrary proteins on and off, wherever and whenever we want.

4

3

89

Andrew York

@AndrewGYork

4 years

When I was a postdoc @NIH , one of my hobbies was trying to answer this question. Grant administrators didn't know, and DIDN'T CARE, what fraction of time their grantees spent pursuing funds. PIs got genuinely angry when I asked them to estimate their grantseeking time fraction.

Ben Reinhardt

@Ben_Reinhardt

4 years

The Szilard point - when more value is wasted applying for a grant than the value of the grant 🤦‍♂️

6

74

224

7

20

86

Andrew York

@AndrewGYork

5 years

From before I joined science-twitter. Good stuff!

Marcel Müller

@mueller_physics

8 years

How structured illumination microscopy extracts extra resolution from the sample ( #fairsim )

1

30

75

1

8

86

Andrew York

@AndrewGYork

6 years

@VirusesImmunity I'm a decade out from my PhD, running my own lab. My PhD advisor was toxic. I'm *still* nervous writing that. No one with any power ever asked my opinion. All I got were awkward questions during my faculty job search, why I changed fields and didn't have a letter from my advisor.

4

2

84

Andrew York

@AndrewGYork

7 years

Our first publication using this method, describing a way to improve STED microscopy: Each interactive figure/animation shows hundreds of "figures" worth of data. All simulation/figure generation code included. #Reproducibility #OpenSource #OpenScience

2

20

82

Andrew York

@AndrewGYork

3 months

Why bother? Why make a magnetically responsive protein? It's actually kinda magical. Light changes AsLOV2's shape; this enables "optogenetics", controlling proteins with light. Unfortunately, humans are opaque. But imagine an antibody drug that turns off with *magnets*....

4

5

80

Andrew York

@AndrewGYork

7 years

Finally, an HTML/CSS/Javascript template, if you want to try it out yourself: It's as simple as forking the @github repo, editing `index.html`, and activating Github Pages. (Your first edit should probably be to remove my name from the author list)

4

19

75

Andrew York

@AndrewGYork

3 years

Hey microscopy/biology twitter: what's the state-of-the art for measuring temperature in a living creature under the microscope? Are there spatially-resolved methods? Fluorescent temperature indicators? Are there precise/trusted approaches, or just noisy/controversial ones?

19

14

70

Andrew York

@AndrewGYork

5 years

I've heard there's "no free lunch" in microscopy; advantages come with tradeoffs. We take this as a personal challenge! Our new microscope design gives the gentleness/speed of lightsheet microscopy, AND the high NA and simple sample prep you're used to with confocal microscopy.

1

13

71

Andrew York

@AndrewGYork

5 years

What about peer review? Real peer review is someone who *tried* it, so we killed two birds (dissemination and peer review) with one stone (a collaboration with @RetoPaul ). Want to know if our design is any good? Want the scoop on how hard it is to build your own? Ask @RetoPaul !

3

2

70

Andrew York

@AndrewGYork

5 years

@joachimgoedhart @WilsonAdams_ Think of an ultrafast laser pulse as a flying pancake. The diffraction grating chops it into French fries, and delays each fry a different amount. The fries spread due to diffraction, the imaging system brings each fry back into focus, equivalent to a picosecond scale line scan.

9

8

70

Andrew York

@AndrewGYork

5 years

I've had a great experience sharing our science via Twitter, better than I ever thought possible. I'm especially grateful to everyone who helped, and I'd like to pay that forward. If you've got some cool science to share, and you'd like me to help spread it, let me know.

2

8

68

Andrew York

@AndrewGYork

5 years

@dopaminator @KaushikLab @arshukla @DeepakNModi @Sandeep_1966 @ViditaVaidya @Sci_Lipi @thattai "Do it yourself" publishing has been LIBERATING. You don't notice how "traditional" publishing warps your approach to science until you leave it behind. Arguably the biggest advantage: I can focus on "how can I advance my field?", rather than "how can I get into a good journal?"

2

11

66

Andrew York

@AndrewGYork

5 years

@OlympusLifeSci I invented this technique. I'd appreciate acknowledgement and citation.

3

1

65

Andrew York

@AndrewGYork

3 years

I want to emphasize for computational folks: this technique is a gold mine of inverse problems. For example, if you're tracking a single particle in 3D, you only need two camera exposures for perfect localization, so you can go thousands of *volumes* per second.

Reto Fiolka

@RetoPaul

3 years

We present rapid projection imaging under variable viewing angles. We apply this method in light-sheet and spinning disk microscopy to visualize 3D samples in real time. We further demonstrate that 3D information can be gathered from a set of projections.

12

113

429

2

9

64

Andrew York

@AndrewGYork

4 years

Microscopy Twitter: I need your help! I'm super proud of @Bin_YANG_Optics and @loicaroyer 's spectacular combination of speed, resolution and gentleness, over a huge volume. But, only three copies of "Big Snouty" currently exist! Should we make more?

Loïc A. Royer 💻🔬⚗️

@loicaroyer

4 years

We are very glad to share our latest preprint on “High-Resolution, Large Field-of-View, and Multi-View Single Objective Light-Sheet Microscopy” where we push the current limits of single-objective light-sheet microscopy. (1/n) @Bin_YANG_Optics et al.

6

92

261

5

14

59

Andrew York

@AndrewGYork

3 months

Last year, we discovered that fluorescent proteins get a little dimmer in modest magnetic fields (e.g. GFP gets ~1% dimmer in ~10 mT). MagLOV gets a LOT dimmer. Here's ΔF/F ≥ 75% in live E. coli! It works purified, and in mammalian cells too.

4

2

59

Andrew York

@AndrewGYork

4 years

Help reunite a scientific couple and launch a career! Meet @David_P_Bauer , a maker&coder&engineer&biologist from @WallaceUcsf ’s lab, looking for biotech|Python|machine learning jobs in Michigan. Want custom fluidics, a Snoutscope, or a smart/kind/hardworking/skilled colleague?

5

26

58

Andrew York

@AndrewGYork

3 years

And just in case you haven't met her, you should go follow @Maria_Ingaramo , the inventor of "relaxation sensing", who lead this team and this project to a pretty smashing success. I've never met someone with more passion for science than Maria. She's the gas in our tanks.

4

0

57

Andrew York

@AndrewGYork

6 years

We're hiring!

3

45

55

Andrew York

@AndrewGYork

3 months

And while you're meeting MagLOV, you should also meet Ashleen Rai ( @RaiAshleen ). Ashleen's been volunteering her nights and weekends, learning protein engineering from @Maria_Ingaramo , and bringing "magnetogenetics" one BIG step closer to reality. She's a joy to work with.

3

2

56

Andrew York

@AndrewGYork

4 years

Who are your favorite folks doing interesting things with data sharing in microscopy (and other fields)? Who has shared data you found useful, or found cool uses for publicly shared data? Please also share your personal stories! cc @HenriquesLab @coppola_s_PhD

25

26

54

Andrew York

@AndrewGYork

6 years

Our third GitHub publication, exploring an apparent paradox in optical measurement: Scientific publications are usually answers; I think there's a lot of value in asking and sharing good *questions*. This is one of my favorites. #openscience

4

11

53

Andrew York

@AndrewGYork

5 years

There's a saying in chess: when you find a good move, look for one that's even better. I'm having a great time at Calico, inventing and discovering in the context of microscopy. But is this the most important way I can spend my life? What else is out there? Open my mind.

11

5

52

Andrew York

@AndrewGYork

5 years

Any scientists out there with an underappreciated paper? Something from your back catalog you wish more people would read? Reply to this thread with a link, or DM me, and I'll retweet it.

11

15

50

Andrew York

@AndrewGYork

5 years

If you're at #FOM2019 , make sure you don't miss the talks by Ben Cooper ("Photoswitching Noise Distorts All Fluorescent Images") and Alfred Millett-Sikking ("A Bolt-on Single-Objective Light-Sheet Design with Uncompromised Numerical Aperture").

2

14

50

Andrew York

@AndrewGYork

4 years

We do everything we can to make true, useful claims about technique development, but the test is how it goes in other labs. Part of me always worries, did I give bad advice? It's so rewarding to see success like this. Congratulations, @kschink et al!

Kay Schink

@kschink

4 years

The first movies from Mr. Snouty in Oslo @CanCell_UiO - beautiful membrane ruffles and endosomes. Some smaller aberrations still present, but we are very happy with it for the first try. @AndrewGYork @amsikking @jsdaniel02 @honeybeeatc @RetoPaul

6

19

118

2

6

47

Andrew York

@AndrewGYork

3 years

Update: @JLazzariDean , @Maria_Ingaramo and I did some followup tests with our @LeicaMicro / @PicoQuant SP8. Congrats to everybody on "team reflection"! Our 20 ns spike was actually at -5 ns, with many hallmarks of laser scattering inside the scanhead.

Andrew York

@AndrewGYork

4 years

Hey microscopy twitter: can you help me track down an artifact? Our @LeicaMicro SP8 with a @PicoQuant lifetime system gives a spike in the lifetime histogram at 20 ns. Anybody know why? I made a github repo with sample data and code to demonstrate:

20

12

36

2

1

48

Andrew York

@AndrewGYork

1 year

Hey Snouty people: micromanager is adding killer features. Consider using it for your snoutscope control!

Tanner Fadero

@TanFad

1 year

@manager_micro Single objective light sheet data (e.g. ) arrives from the detector “skewed.” Example below: the horizontal and vertical image dimensions are orthogonal to each other, but the slice dimension isn’t perfectly orthogonal to the vertical image axis. (2/7)

1

3

9

0

3

46

Andrew York

@AndrewGYork

1 year

New photophysics unlocks new inventions, like background rejection (blinking magnetofluors vs. nonblinking background) or multiplexing (different mutants equilibrate at different rates). Long-term, we're dreaming of "magnetogenetics": magnetic control of optogenetic circuits!

2

1

47

Andrew York

@AndrewGYork

3 years

Roll call! Who's got a Snouty? How's it going? How are you doing your alignment? What approach are you taking for software? Which hardware choices did you make? We've done a lot of one-on-one calls, but I love crosslinking. ...maybe even a conference?

Andrew York

@AndrewGYork

5 years

Microscopy technique development's exploding, but core facilities still buy confocals. This ugly baby will end that. Less phototoxicity, WAY faster than confocal. NO DRAWBACK. Details here: Co-invented by @amsikking . Get one from jon @asiimaging .com

40

338

869

8

9

46

Andrew York

@AndrewGYork

5 years

Super impressed to learn that @dmahecic made a homebrew iSIM. That thing is damn hard to build, and it looks like she massively improved on my design. Respect! I feel guilty that I didn't provide any help or warnings, but obviously she didn't need it!

2

3

45

Andrew York

@AndrewGYork

5 years

Our design uses ALMOST all stock parts. There's one custom lens, invented at Calico, manufactured by @SpecialOptics , and distributed by @ASIImaging . Help ASI commission a large (cheap!) batch by telling @jsdaniel02 you're interested! Email: jon @asiimaging .com

6

45

Andrew York

@AndrewGYork

5 years

(...also we really need help naming this objective. I can't keep calling it "Mr. Snouty" forever, right?)

11

0

44

Andrew York

@AndrewGYork

6 years

@alexcarisey @christlet @maxadrian @HenriquesLab @Cairn_GRog @tlambert03 @Cairn_Research @VisiTech_UK Pinhole-closing methods: Leica Hyvolution, Olympus SR 10, and (I suspect) Roper liveSR Digital reassignment methods: Enderlein's ISM, Zeiss Airyscan, my MSIM, ONI SIM Optical reassignment methods: my instant SIM, Mander's rescan confocal, vt-iSIM, Rainer's OPRA, Yokogawa SoRa.

5

18

44

Andrew York

@AndrewGYork

5 years

Snouty, but ~3x the field of view, 10° more tilt range, and no tradeoffs. Prototype for now, but help persuade @ASIImaging to commission a large (=cheap) batch by telling @jsdaniel02 you're interested. I'm guessing ~2x the price? More importantly: NAMING CONTEST!

Alfred Millett-Sikking

@amsikking

5 years

Hail #KingSnout ! The latest member of the family! The (prototype) AMS-AGY v2.0 single-objective light-sheet lens from @Calico . Everything you love about Snouty v1.0, with a HUGE FIELD! Want one? Email @jsdaniel02 at ASI! They need lots of interest to order a big (cheap) batch!

7

28

103

12

7

43

Andrew York

@AndrewGYork

5 years

There's a global conspiracy to conceal the fact that GFP emits a fucking ORDER OF MAGNITUDE fewer photons before photobleaching if you excite with 2-photon instead of 1-photon. (This angry evidence-free assertion brought to you by Cunningham's Law. Fight me!)

10

1

42

Andrew York

@AndrewGYork

3 months

@Maria_Ingaramo and @RaiAshleen made MagLOV out of an oat-plant protein called AsLOV2. Each round, they screen ~3000 single-mutants, and select for enhanced magnetofluorescent response. Wild-type AsLOV2 has almost no magnetic response, but only five mutations got us to ~75%!

3

2

41

Andrew York

@AndrewGYork

1 year

Modest (~mT) fields can give huge (~80%) magnetomodulation for a chemical fluorophore in nonaqueous solvent: @AdamEzraCohen ...but previously known biorelevant/biocompatible magnetoeffects are weak and exotic (e.g. cryptochrome transient absorption).

3

7

40

Andrew York

@AndrewGYork

4 years

I've had a great experience so far with open peer review. So much of review is teaching the reviewer the paper's content, and teaching the authors the reviewer's misunderstanding. Teaching is inherently iterative; why iterate in months when you can iterate in minutes?

Suliana Manley 🔬🗜🧫

@SulianaManley

4 years

Our paper was greatly improved through feedback from reviewers; we got to experience our first open peer review with microscopist extraordinaire @AndrewGYork . Inspired by our convos, Dora and Khalid did some experiments to show how homogeneity builds up as speckles are averaged

2

1

13

1

3

40

Andrew York

@AndrewGYork

6 years

My favorite collaboration at Calico is recruiting: The scientist leading this project is someone I respect and trust tremendously. PhD not required; experience and passion for microscopy, coding, automation, and cell biology is what we're looking for.

Careers - Calico

www.calicolabs.com

3

31

40

Andrew York

@AndrewGYork

5 years

@CellJeffe @christlet @MolinesArthur @uwmicroscopy @HenriquesLab Short answer: They're misinterpreting a common artefact; converged iterative deconvolution shows tiny structures whether or not the sample contains them. Nuanced answer: there's a fun/open question about the interplay between the band limit and the nonnegativity prior...

1

4

38

Andrew York

@AndrewGYork

4 years

I find if you do it right, tech dev IS basic research, with the added benefit that at the end, not only do you understand something fundamental, you also have a useful new tool. Most of my research follows (or tries to follow) this pattern.

Ricardo Henriques

@HenriquesLab

4 years

Gets told by a peer the usual "tech is not research" speach. Gets big tech research paper accepted the same day =)

14

8

180

3

38

Andrew York

@AndrewGYork

3 years

I had the good fortune to hear @loicaroyer playing piano this weekend. I love music, but I know nothing of piano, so I was delighted when he opened with one of the better songs I've ever heard. I felt real emotion. I wanted the song name, but turns out he was improvising!

3

0

38

Andrew York

@AndrewGYork

3 years

@ProfTomEllis Me, it's going great. There's an unfortunate false equivalence here though. I haven't published via journals for years, but I'd say my work is more thoroughly peer reviewed than anyone I know. Real peer review is when people try to build on your work.

3

4

36

Andrew York

@AndrewGYork

6 years

Happy to be spending my evening reading the MoNaLISA paper from @IlariaTesta4 's crew: I usually just skim titles and abstracts, but it's nice to dig into the actual text sometimes :-D

Enhanced photon collection enables four dimensional fluorescence nanoscopy of living systems

Nature Communications - Super-resolution microscopy often suffers from low contrast and slow recording times. Here the authors present an optical implementation which makes the fluorescent...

www.nature.com

2

7

37

Andrew York

@AndrewGYork

5 years

@NBioimaging @Bin_YANG_Optics @naturemethods I'm especially grateful to the authors for preprinting the work. Their innovation changed the course of our research program, and the preprint gave us more than a year's head start compared to standard publishing.

High Numerical Aperture Epi-illumination Selective Plane Illumination Microscopy

Selective-plane illumination microscopy (SPIM) provides unparalleled advantages for long-term volumetric imaging of living organisms. In order to achieve high-resolution imaging in common biological...

www.biorxiv.org

2

37

Andrew York

@AndrewGYork

4 years

I agree with this whole thread

Aquiles Carattino

@aquicarattino

4 years

Scientific hardware companies are sometimes jealous of their software to the point of not even documenting the API's they use. For most users, this is not a specific concern, since things 'just work', for few users it is a nightmare.

1

5

65

6

7

36

Andrew York

@AndrewGYork

5 years

Got a delightful (unsigned) surprise gift! If I'm right about who sent it, they'll see this message from me: YOU'RE AWESOME! You brightened my week, and I'm glad I know you. Looking forward to seeing you again in July!

0

35

Andrew York

@AndrewGYork

4 years

Hey microscopy twitter: can you help me track down an artifact? Our @LeicaMicro SP8 with a @PicoQuant lifetime system gives a spike in the lifetime histogram at 20 ns. Anybody know why? I made a github repo with sample data and code to demonstrate:

20

12

36

Andrew York

@AndrewGYork

5 years

@HenriquesLab Use my line: "I've always believed that scientists (gesture humbly to myself) and biologists (gesture benevolently to them) should work together as if they were equals. I don't care what anybody says, biologists *can* be taught." Then play reaaal dumb.

1

0

35

Andrew York

@AndrewGYork

1 year

A little bit of my favorite kind of peer review here: the kind with data!

Adam Cohen

@AdamEzraCohen

1 year

@AndrewGYork @JoeMcAuliffe17 Yup. I was very skeptical, but two people in my lab have independently reproduced the magnetic field effect for mScarlet expressed in E. coli. I'm convinced enough to keep exploring.

1

2

32

3

0

35

Andrew York

@AndrewGYork

5 years

Finally, a big shoutout to @amsikking . Alfred's an awesome optical engineer (and physicist, microscopist, builder, colleague, friend...). I'm lucky to work with him at Calico. He's also new to Twitter. You should follow him!

3

0

34

Andrew York

@AndrewGYork

3 years

Maria spent years making a photoactivatable fluorescent protein that rapidly spontaneously "relaxes". She uses the "relaxation rate" to read her biosensors. This is incredibly robust: her pH sensor still reads accurately underneath a *millimeter* of chicken skin!

2

3

35

Andrew York

@AndrewGYork

6 years

Hey microscopy Twitter: what are your favorite examples of highly optimized fluorescent protein biosensors? I'm interested in sensors (beyond GCaMP) that have been through multiple rounds of iterative improvement to get really awesome performance.

12

16

34

Andrew York

@AndrewGYork

5 years

Can we make a "stimulated emission contrast" microscope? It's such a simple question, but we couldn't find an answer in the literature. So we did the experiment! (and a LOT of controls)

2

4

33

Andrew York

@AndrewGYork

3 years

I'm loving this article by @AdamEzraCohen et al! I'm especially excited about their suggestion: "...excited state Rayleigh scattering could be made directional via a transient grating arrangement." This isn't just an idea, it's an idea factory!

Which way does stimulated emission go?

Is it possible to form an image using light produced by stimulated emission? Here we study light scatter off an assembly of excited chromophores. Due to the Optical Theorem, stimulated emission is...

arxiv.org

3

8

32

Andrew York

@AndrewGYork

1 year

Another update: a wonderful gift from an amazing scientist/artist, @ChizhikAlexey ! He made us this beautiful cover art! I'm so impressed, pleased, and grateful. I love having friends like this :⁠-⁠)

2

0

32

Andrew York

@AndrewGYork

5 years

@florianjug @MBLPhys Student 2011, lead directly to my current PI position. Also broke me down into component pieces and restarted my life from scratch. I'd never been surrounded by competence and inspiration before, and I'd never felt so happy or so right in a tribe.

1

2

32

Andrew York

@AndrewGYork

3 years

Normal fluorescent biosensors "readout" by changing brightness or lifetime. This works in transparent single cells, that have no autofluorescent background. Animals like worms, flies, and mice ALWAYS have background :( ...but *relaxation rate* measurements ignore background :D

2

0

31

Andrew York

@AndrewGYork

4 years

Agree! In the same spirit, don't use "institutional" email for "corresponding author", use your real one. Using email as a redundant way to signal affiliation is silly. The point of an email address is, folks can contact you. The acceptable excuse for email linkrot is you died.

Oded Rechavi

@OdedRechavi

4 years

In my opinion, in most cases, it makes sense to also make the first author a corresponding author

58

77

1K

5

3

31

Andrew York

@AndrewGYork

6 years

What's missing from science Twitter? My answer: I see polished results (preprints, publications), but almost no in-progress science! Can we do better? Reply with examples of your favorite open questions, fresh ideas, and live discoveries. Here's mine:

Andrew York

@AndrewGYork

6 years

Our third GitHub publication, exploring an apparent paradox in optical measurement: Scientific publications are usually answers; I think there's a lot of value in asking and sharing good *questions*. This is one of my favorites. #openscience

4

11

53

2

11

31

Andrew York

@AndrewGYork

5 years

@kanderson @CT_Bergstrom @KjblackJohn Everything you just said is (impressively) wrong. You obviously have no idea what you're talking about. A lot of smart people with more patience than me are making a good faith effort to educate you. Read their replies and try to learn from them. You're welcome.

0

31

Andrew York

@AndrewGYork

7 years

@NicoPC131 Because I'm in this happy position, I feel an obligation to take the chance I've been given, and do what I think is right. Hopefully our examples help establish that this approach is legitimate, and reduce the professional risk for others who want to try it out.

0

30

Andrew York

@AndrewGYork

5 years

@biorxivpreprint I don't think this work is appropriate for biorxiv. If you're unfamiliar with biorxiv, please don't judge biorxiv by this preprint; I don't think this is a typical or representative preprint. Also, please don't assume that biorxiv endorses the contents of this work.

2

0

29

Andrew York

@AndrewGYork

4 years

2. I think job interviews are almost worthless. "Can you stay charming and seem smart for six hours straight?" doesn't select for "will we inspire mutual creativity, hard work, and joy in each other?"

1

2

28

Andrew York

@AndrewGYork

5 years

A key innovation for bespoke designs: trivially assembled "custom" lenses! A Mr. Snouty light-sheet needs juuust the right mag, but off-the-shelf tube lens focal length selection is limited. No problem! Follow our recipe to bang together a few @Thorlabs lenses Lego-style.

1

10

29

Andrew York

@AndrewGYork

5 years

Finally, meet the fearless physicist willing to tackle this kind of question: @sanjay_r_varma Sanjay's a deft hand with paradoxes and plasmas and Python, and is brand new to Twitter. Follow him! We're hoping this paper raises a lot of questions. Ask him!

4

1

28

Andrew York

@AndrewGYork

6 years

My awesome colleague @jacobkimmel whipped up a Python/Numpy implementation of periodic/smooth decomposition! (I predict a bright future for Jacob; he picks things up *fast*.)

3

4

28

Andrew York

@AndrewGYork

6 years

I'm proud to be the first Twitter follower for @SusanSuperRes . She's one of the smartest and most creative microscopists working today, and I always learn something reading her work. Follow her!

3

6

28

Andrew York

@AndrewGYork

3 years

And let me shoutout to @ZumraSeidel , who joined the project just in time for the pandemic. She's brilliant, and a true pleasure to work with. Her passion for GETTING SH*T DONE and the genuine delight she brought to science were infectious, it was a privilege to work with her.

1

0

28

Andrew York

@AndrewGYork

5 years

@hpke1980 @manorlaboratory GitHub and Biorxiv! Then after your tweetstorm about it, let the journal editors chase *you*.

2

4

28

Andrew York

@AndrewGYork

3 years

Much to our delight, it worked on the first try! We measure a *quantitative* pH change in the mitochondria, in the tumor, in response to a mitochondria-specific drug - accurately! The mouse is optically horrible - opaque, autofluorescent, and wiggly, but the sensor still works.

1

27

Andrew York

@AndrewGYork

5 years

I'm very, very excited about this objective. With a sufficiently high NA, large FOV, and insensitivity to refractive index, why would you ever use a second objective?

Jon Daniels

@jsdaniel02

5 years

Announcing plans for our 3rd multi-immersion objective: 48x/1.05 in water or 56x/1.22 in ECi, 3mm WD, 0.5mm FOV. Uses include lattice LS, high-NA cleared tissue, and SOLS. Fits in mechanical envelope of Nikon 25x/1.1w. Contact me if interested. Details at .

4

14

61

0

2

26