Name: leafj: an imagej plugin for semi-automated leaf shape measurement
Uploaded: 2013-01-21T12:00:00
Description: Watch this Scientific Journal Video about LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement at JoVE.com

LeafJ blev skrevet af JNM mens han var på orlov i Dr. Katherine Pollard laboratorium på Gladstone institutter. Dette arbejde blev støttet af en bevilling fra National Science Foundation (tilskud nummer IOS-0.923.752).

1. Plantematerialer Bemærk, at denne plante vækst Protokollen skal til detektering skygge avoidance response. Du kan dyrke planter under din favorit tilstand. <ol><li> Drys Arabidopsis thaliana frø på vand gennemvædet filtrerpapirarkene i 9 cm petriskåle og gemme (stratificere) dem ved 4 ° C i fire dage i mørke. </li><li> Overføre disse petriskåle til simulerede solforhold: 80-100 μE fotosyntetisk aktiv stråling (PAR) og langt-rød supplement til bringe R: FR-forholdet...

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Vores &quot;LeafJ&quot; plugin muliggør måling af stilk længde semi-automatisk, hvilket øger throughput næsten 6 gange over manuel måling. Bladstilken længde er en vigtig indeks i SAS og er også et vartegn for andre fænomener, såsom nedsænkning modstand og hyponastic vækst 17. Derfor dette plugin kan være nyttig til en lang række planteforskere. Vores plugin er implementeret i et veletableret java-baseret gratis software, ImageJ. Dette gør det nemt at cross-platform...

<html><table border="1"><tbody><tr><td> Navn på reagenset </td><td> Firma </td><td> Katalognummer </td><td></td></tr><tr><td> langt rødt lys LED </td><td> Orbitec </td><td> skræddersyet </td><td></td></tr><tr><td> gennemsigtighed </td><td> IKON </td><td> HSCA / 5 </td><td></td></tr><tr><td> scanner </td><td> Epson </td><td> Epson Perfection V700 PHOTO </td><td></td></tr><tr><td> Billede J </td><td> NIH </td><td></td><td> <a href="http://rsbweb.nih.gov/ij/" target="_blank">http://rsbweb.nih.gov/ij/</a> </td></tr><tr><td> LeafJ </td><td> custom </td><td></td><td> <a href="http://www.openwetware.org/wiki/Maloof_Lab" target="_blank">http://www.openwetware.org/wiki/Maloof_Lab</a> </td></tr><tr><td> Air Display </td><td> Avatron Software Inc. </td><td></td><td>blank &quot;&gt; http://avatron.com/ </td></tr><tr><td> iPad2 </td><td> Apple Inc. </td><td></td><td> <a href="http://www.apple.com/" target="_blank">http://www.apple.com/</a> </td></tr></tbody></table>

leafj: an imagej plugin for semi-automated leaf shape measurement

High throughput fænotypebestemmelse (phenomics) er et effektivt værktøj til at forbinde gener til deres funktioner (se anmeldelse 1 og nylige eksempler 2-4). Bladene er den primære fotosyntetiske organ, og deres størrelse og form varierer developmentally og miljømæssigt i en plante. Af disse grunde undersøgelser af blad morfologi kræver måling af flere parametre fra mange blade, som gøres bedst ved halvautomatiske phenomics værktøjer 5,6. Canopy skygge er et vigtigt miljømæssigt cue, der påvirker plante arkitektur og livshistorie, den suite af svarene er samlet kaldes skygge unddragelse syndrom (SAS) 7. Blandt SAS responser, er skygge induceret Bladstilken forlængelse og ændringer i bladet område særligt anvendelige som indeks 8. Til dato, kan bladform programmer (f.eks SHAPE 9, LAMINA 10, LeafAnalyzer 11, LEAFPROCESSOR 12) måle blad konturer og kategorisere bladformer, Men kan ikke udsende bladstilk længde. Mangel på store målesystemer af blade bladstilke har hæmmet phenomics tilgange til SAS forskning. I denne artikel beskriver vi et nyudviklet ImageJ plugin, kaldet LeafJ, der hurtigt kan måle bladstilk længde og bladplade parametre i modellen planten Arabidopsis thaliana. For den lejlighedsvise blad, der krævede manuel korrektion af stilk / bladpladen grænse brugte vi en touch-screen tablet. Endvidere blad celleform og blade celleantal er vigtige determinanter for blad størrelse 13. Adskilt fra LeafJ vi også præsentere en protokol for at bruge en touch-screen tablet til måling af celleform, område og størrelse. Vores blad træk målesystem er ikke begrænset til skygge-unddragelse forskning og vil accelerere blad fænotypebestemmelse af mange mutanter og screening planter ved blad fænotypebestemmelse.

1. Leaf Images Viser Skøn af Bladstilk og Leaf Blade Boundary, og deres Måling Vindue En af de mest nyttige funktioner i LeafJ er automatiseret detektering af bladpladen / bladstilken grænse (Figur 1). The LeafJ algoritme fungerer på følgende måde: den indbyggede ImageJ ParticleAnalyzer funktionalitet anvendes til at finde og bestemme orienteringen af ​​bladene inde i brugerens valg. For hvert blad bredden af ​​bladet bestemmes langs bladet samlede akse. Derefter ...

Watch this Scientific Journal Video about LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement at JoVE.com

LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement

Demonstration af de vigtigste metoder til high throughput blad målinger. Disse metoder kan anvendes til at accelerere blad fænotypebestemmelse når man studerer mange plante mutanter eller på anden måde screening planter ved blad fænotype.

LeafJ: En ImageJ Plugin til Semi-automatiseret Leaf Shape Måling

High throughput phenotyping (phenomics) is a powerful tool for linking genes to their functions (see review1 and recent examples2-4). Leaves are the ...

Research

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