Hamamatsu

Welcome to The Living Image, a website celebrating the little things in life.

TECHNICAL GUIDES

Relative SNR—How does your camera compare?

Compare microscope cameras or understand how specs affect performance.
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How many photons do I have?

Find out how to measure how many photons are present under your experimental conditions.
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Calculating SNR

Understand the different components that go into calculating the signal-to-noise ratio (SNR).
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A visual guide to CCD vs. EM-CCD vs. CMOS

Different chip architectures, different capabilities.
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Changing the Game

An in-depth look at how the new Gen II sCMOS technology reduces tradeoffs between speed and sensitivity. (PDF)
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Contrast versus noise, eye versus machine.

Contrast appears good, but good looks can be deceiving.
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What is dark noise?

A basic introduction.
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Dissecting camera specifications: a field guide for biologists

Shedding light on what camera specifications mean for biological experiments.
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Bridging the Gap

The impact and correction of camera noise for computational microscopy including precision localization nanoscopy (PDF).

Read noise in CMOS cameras: only rms is meaningful

A brief overview of median versus rms read noise for evaluating CMOS cameras.
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Thinking in Photons.

Converting from electrons to photons improves how we think about signal-to-noise ratio (SNR).
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Which camera technology is right for me?

Choosing between CCD, EM-CCD, and sCMOS.
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User Guides

The Time Sensitive Experiment

A decision tree for visualizing biology in action using the ORCA-Flash 4.0.
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Camera Simulation Engine Enables Efficient System Optimization for Super-Resolution Imaging.

 Stephanie Fullerton ; Keith Bennett ; Eiji Toda ; Teruo Takahashi. SPIE , 822811 (February 9, 2012); doi:10.1117/12.906346

It's all about noise and how you deal with it.

An overview of why Huang, et al, (2013), generated new software algorithms for precision localization (using SMSN) with an sCMOS camera.
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Can You Trust What You See?

A short guide to reliable microscopy imaging.
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Capturing images you can count on.

A checklist for microscopy imaging.
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Publications

ORCA-Flash4.0

Vettenberg, et al. Light-sheet microscopy using an Airy beam. Nat Methods. 2014 Apr 6. 11:541-544. PMID: 24705473.
Ahrens, MB, et al. Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat Methods. 2013 May;10(5):413-20. PMID: 23524393
Huang, F, et al. Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms. Nat Methods. 2013 Jul;10(7):653-8.  PMID: 23708387

ORCA-flash2.8

Huang, ZL, et al. Localization-based super-resolution microscopy with an sCMOS camera. Opt Express. 2011 Sep 26; 19(20):19156-68. PMID: 21996858
Basler, M, et al. Type VI secretion requires a dynamic contractile phage tail-like structure. Nature. 2012 February 26; 483(7388): 182–186. PMCID: PMC3527127
Saurabh, S, et al. Evaluation of sCMOS cameras for detection and localization of single Cy5 molecules. Opt Express. 2012 March 26; 20(7): 7338–7349. PMCID: PMC3500109

ImagEM

Meseroll, RA, et al. Septin Phosphorylation and Coiled-Coil Domains Function in Cell and Septin Ring Morphology in the Filamentous Fungus Ashbya gossypii. Eukaryot Cell. 2013 February; 12(2): 182. PMCID: PMC3571309
Turner, RD, et al. Cell wall elongation mode in Gram-negative bacteria is determined by peptidoglycan architecture. Nat Commun. 2013 February 19; 4: 1496. PMCID: PMC3586723
Lauria, I, et al. GLTP Mediated Non-Vesicular GM1 Transport between Native Membranes. PLoS One. 2013; 8(3): e59871.  PMCID: PMC3610762
Dhungel, B, et al. Baculovirus-mediated gene transfer in butterfly wings in vivo: an efficient expression system with an anti-gp64 antibody. BMC Biotechnol. 2013; 13: 27.  PMCID: PMC3614531
Okada, S, et al. Daughter Cell Identity Emerges from the Interplay of Cdc42, Septins, and Exocytosis. Dev Cell. 2013 July 29; 26(2): 148. PMCID: PMC3730058
Younghoon, O, et al. Targeting and functional mechanisms of the cytokinesis-related F-BAR protein Hof1 during the cell cycle. Mol Biol Cell. 2013 May 1; 24(9): 1305. PMCID: PMC3639043
Hayashi, T, et al. IL1RAPL1 Associated with Mental Retardation and Autism Regulates the Formation and Stabilization of Glutamatergic Synapses of Cortical Neurons through RhoA Signaling Pathway. PLoS One. 2013; 8(6): e66254.  PMCID: PMC3681934
Montieth, A, et al. Imaging of Mitochondrial and Non-Mitochondrial Responses in Cultured Rat Hippocampal Neurons Exposed to Micromolar Concentrations of TMRM. PLoS One. 2013; 8(3): e58059.  PMCID: PMC3587568
Correa, P, et al. Dopaminergic D2-Like Receptors Delimit Recurrent Cholinergic-Mediated Motor Programs during a Goal-Oriented Behavior. PLoS Genet. 2012 November; 8(11): e1003015. PMCID: PMC3499252
Wallace BT, et al. Lateral mobility of L-type calcium channels in synaptic terminals of retinal bipolar cells. Mol Vis. 2013; 19: 16–24. PMCID: PMC3548577

ORCA-R2

0
Aguilar, A, et al. Analysis of human samples reveals impaired SHH-dependent cerebellar development in Joubert syndrome/Meckel syndrome. Proc Natl Acad Sci USA. 2012 October 16; 109(42): 16951–16956. PMCID: PMC3479472
Nussbaum-Krammer, CI, et al. Spreading of a Prion Domain from Cell-to-Cell by Vesicular Transport in Caenorhabditis elegans. PLoS Genet. 2013 March; 9(3): e1003351. PMCID: PMC3610634
1
Schaub, JR, and Stearns, T. The Rilp-like proteins Rilpl1 and Rilpl2 regulate ciliary membrane content. Mol Biol Cell. 2013 February 15; 24(4): 453–464. PMCID: PMC3571868
Takaba, H, et al. A major allogenic leukocyte antigen in the agnathan hagfish. Sci Rep. 2013; 3: 1716. PMCID: PMC3634110
2
Chandsawangbhuwana, C, et al. High-throughput optofluidic system for the laser microsurgery of oocytes. J Biomed Opt. 2012 January; 17(1): 015001. PMCID: PMC3380719
Yan, X, et al. Optical Imaging of Tumors with Copper-Labeled Rhodamine Derivatives by Targeting Mitochondria. Theranostics. 2012; 2(10): 988–998. PMCID: PMC3493204
3
Akita, T, and Okada, Y. Regulation of bradykinin-induced activation of volume-sensitive outwardly rectifying anion channels by Ca2+ nanodomains in mouse astrocytes. J Physiol. 2011 August 15; 589(Pt 16): 3909–3927. PMCID: PMC3179992
Al-Omari, M, et al. Acute-Phase Protein α1-Antitrypsin Inhibits Neutrophil Calpain I and Induces Random Migration. Mol Med. 2011 Sep-Oct; 17(9-10): 865–874. PMCID: PMC3188872
4
Van Zoggel, H, et al. Antitumor and Angiostatic Activities of the Antimicrobial Peptide Dermaseptin B2. PLoS One. 2012; 7(9): e44351. PMCID: PMC3447859
Basler, M, et al. Type VI secretion requires a dynamic contractile phage tail-like structure. Nature. 2012 February 26; 483(7388): 182–186. PMCID: PMC3527127

Hamamatsu Journal Club

Dynamin2 helps organize actin networks in cell migration

How do cells migrate? A network of interdependent actin filament structures shift and remodel...
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Use it or lose it: Mechanically activated cation channel essential to heart health

How does the heart respond to mechanical stress? The physical load and mechanical stresses of pumping blood are crucial to...
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Combined techniques identifyy proteins specific to lipid droplets in S. cerevisiae

How can researchers identify the specific network of biomolecules responsible for the structure and functions of an intracellular organelle?
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Threat alert: Actin enzyme inhibition mediates innate immune signaling in Arabidopsis

How do cells activate a response to pathogen detection? Plant and animal cells recognize potential invaders in part by...
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Piecing it together: New technique locates DNA breaks

How are double-strand breaks caused in genomic DNA?
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Fat or lean? Atlastin links ER to lipid storage

What determines the size of lipid droplets for fat storage?
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Reaching out: Myosin XIK aids root hair elongation in Arabidopsis

What role do myosins play in the growth of plan root hairs?
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Close associates: ER connection aids mitochondria in Neurospora crassa

How does association with the endoplasmic reticulum influence mitochondrial function?
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Growing roots: Plant cues invite helpful bacteria to move in

How does the beneficial bacterium Bacillus subtilis colonize plant roots?
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Positive feedback: Both gene inhibition and activation mark time in Arabidopsis

How does the model plant Arabidopsis thaliana maintain its circadian clock?
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Seeing the light: Model system probes photoperiod gene response

How do mammals adjust their physiology to suit the seasons?
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Tracing β cell origins

How does the adult pancreas produce new β cells?
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Remodeling the membrane during cellularization in Drosophila

How is cell cleavage organized in developing embryos?
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All in the family: Plant and animal pathogens share virulence gene

How do parasitic bacteria establish a presence within live host cells?
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Energy alternatives: Metabolic cues regulate algal gene expression

How do cells co-ordinate metabolic activity to suit available energy sources?
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Layer by layer—Formation of bacterial biofilms

What forces shape the early growth of a bacterial biofilm?
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Getting a clear message: Duo regulates signal protein levels in cilia

How do cells control movement of signaling proteins into and out of key organelles?
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Like mother, like daughter—New microtubule arrays align to mimic parent cell

How do cells establish the orientation of cortical microtubules, and therefore the direction of cell growth, after mitosis?
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Membrane maintenance: Regulation of lipid synthesis in S. cerevisiae

What factors regulate lipid metabolism and membrane dynamics in Saccharomyces cerevisiae?
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Positioned for growth: Mechanical forces help cells find their place in early embryos.

How to cells in new embryos position themselves for further growth?
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New signaling pathway culpable in Beta-amyloid neurotoxicity

How does beta-amyloid lead to neuronal death in Alzheimer's Disease?
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With a little help from a friend: Discovering a new protein partnership in cell division

How do nuclear proteins choreograph chromosome movement in mitosis and meiosis?
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Visualizing protein complex movement in plant cell walls

How do plant cells manage cellulose addition and organization during cell growth?
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Who has the beat? Imaging subcellular calcium concentrations over rapid time scales.

What physiological changes in the cell contribute to the beat-to-beat variability in heart rate?
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Quantifying protein interactions in vivo

How do you measure protein-protein interactions in their native environment—that is, inside a living cell?
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Seeing chromosome segregation in bacteria

How do bacterial cells ensure each daughter cell gets one and only one copy of the chromosome during cell division
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