LeafJ a été écrit par JNM alors qu&#39;il était en congé sabbatique au laboratoire du Dr Katherine Pollard aux Instituts Gladstone. Ce travail a été soutenu par une subvention de la National Science Foundation (numéro de licence IOS-0923752).

1. Matières végétales Notez que ce protocole a pour objectif la croissance des plantes pour détecter la réaction d&#39;évitement ombre. Vous pouvez faire pousser des plantes dans votre état préféré. <ol><li> Saupoudrer de graines d&#39;Arabidopsis thaliana sur l&#39;eau trempés papiers filtres dans 9 des plats de Pétri et magasins cm (stratification) les à 4 ° C pendant quatre jours dans l&#39;obscurité. </li><li> Transférer ces boîtes de Pétri à conditions d&#39;ensoleillement simulées: 80-100 rayonnement pE photosynthétiquement actif (RPA) et rouge lointain supplément pour amener le R: FR rapport à 1,86. Utiliser conditions de jours longs (16 h de lumière / 8 h obscurité) et la température constante de 22 ° C. Incuber dans cet état pendant trois jours pour permettre aux graines de germer. </li><li> Transfert de graines germées au sol et garder les plantes dans des conditions dim. Pour les grandes expériences, nous vous recommandons de préparer de petites étiquettes pour l&#39;étiquetage chacune des plantes à l&#39;aide de Gestionnaire de fusion de données dans Microsoft Word 2004 (ou version ultérieure) pour créer des étiquettes. </li><li> Onze jours après transfer sur le sol, placez la moitié des plantes à l&#39;état de l&#39;ombre: même soleil, mais avec droit de reprise rouge lointain lumière pour ramener le ratio R / FR à 0,52. </li><li> Après une période de douze jours, les plantes sont prêtes pour l&#39;imagerie feuille. A ce stade, les feuilles les plus âgées ont pleine maturité alors que les jeunes feuilles sont toujours en expansion, de sorte que vous capturer un instantané de développement. Vous pouvez choisir un temps de développement différent en fonction de vos besoins. </li></ol> 2. Capture d&#39;images feuilles disséquées <ol><li> Préparer les feuilles de transparence étiquetés avec génotype de la plante et des conditions de croissance avec cinq cadres rectangulaires. Un cadre correspond à feuilles d&#39;une plante. Microsoft Excel peut être utilisée pour imprimer une grille conforme aux étiquettes. </li><li> Disséquer feuilles de 26 jours vieilles usines. </li><li> Balayage part à 600 dpi sur un scanner à plat. Notez que laisse d&#39;une plante doit être placée verticalement dans une fenêtre noire dans un sandwich de feuilles transparentes. Évitez de toucher les feuillespour un cadre de fenêtre noire et feuilles qui se chevauchent, ce qui donnera une erreur, les procédures suivantes. </li></ol> 3. Feuille d&#39;analyse d&#39;images par LeafJ <ol><li> Télécharger ImageJ Faites glisser le fichier LeafJ.jar dans le dossier plugins d&#39;ImageJ. </li><li> Ouvrir un fichier image en 1.45s ImageJ ou tard, 14. </li><li> Diviser l&#39;image en trois couleurs canaux (rouge, vert et bleu) par &quot;Image&gt; Couleur Canaux&gt; Split&quot; et appliquer seuil à l&#39;image dans le canal bleu. </li><li> Sélectionner toutes les feuilles d&#39;une plante par un outil rectangle (figure 1A). </li><li> Sélectionnez &quot;LeafJ&quot; dans le menu plugin. </li><li> Sélectionnez informations d&#39;annotation pour cette plante à partir de la boîte de dialogue qui apparaît. Vous pouvezmodifier les valeurs par défaut qui apparaissent ici en cliquant sur &quot;modifier ces options&quot;. </li><li> Après l&#39;exécution de plug-in LeafJ et avant de cliquer sur &quot;OK&quot;, modifier les lignes tracées de la région de fenêtre du gestionnaire d&#39;intérêt (ROI) (si nécessaire; figure 1B). Une tablette à écran tactile (comme un iPad) est utile pour cette procédure. iPads peut être connecté à un ordinateur comme un moniteur externe en utilisant un logiciel d&#39;affichage de l&#39;air. </li><li> Exporter les résultats de mesure et les informations associées (nom de fichier, le temps de la floraison, disséqués par mesurées par, etc) vers Microsoft Excel ou un logiciel équivalent. </li></ol> 4. Feuille d&#39;analyse d&#39;images de cellules dans ImageJ <ol><li> Fixer disséqué laisse comme décrit dans la référence 15 après la numérisation (étape 2). Feuilles FAA fixes peuvent être conservés dans 4 ° C pendant au moins 6 mois. </li><li> Effacer les feuilles en changeant fixateur FAA à la solution de l&#39;hydrate de chloral et les feuilles incuber pendant 1 à 2 heures avant l&#39;observation microscopique 15. </li><li> Mont quitte le microscope glisse avec trichomes vers le haut. En utilisant un grossissement 40x sur un microscope optique, l&#39;image de la couche de mésophylle le centre de chaque feuille de chaque côté de la nervure principale, en évitant les cellules proches de trichomes ou des veines. </li><li> Cellule de feuille de trace décrit par l&#39;outil ImageJ gestionnaire retour sur investissement avec l&#39;aide de la tablette à écran tactile et un stylet (comme décrit dans l&#39;étape 3). Cellule d&#39;analyse d&#39;image utilise les fonctionnalités intégrées de ImageJ mais n&#39;exige pas LeafJ. </li></ol>

<ol>
	<li>Furbank, R. T., Tester, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phenomics--technologies+to+relieve+the+phenotyping+bottleneck.">Phenomics--technologies to relieve the phenotyping bottleneck.</a> Trends Plant Sci. 16, 635-644 (2011).</li><li>Berger, B., Parent, B., Tester, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+shoot+imaging+to+study+drought+responses.">High-throughput shoot imaging to study drought responses.</a> J. Exp. Bot. 61, 3519-3528 (2010).</li><li>Borevitz, J. 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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Shade+Avoidance.">Shade Avoidance.</a> The Arabidopsis Book. , e0157 (2012).</li><li>Smith, H., Kendrick, R. E., Kronenberg, G. H. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Photomorphogenesis in Plants. , 377-416 (1994).</li><li>Iwata, H., Ukai, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SHAPE:+a+computer+program+package+for+quantitative+evaluation+of+biological+shapes+based+on+elliptic+Fourier+descriptors.">SHAPE: a computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors.</a> J. 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D., Magalhaes, P. J., Ram, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Image+Processing+with+ImageJ.">Image Processing with ImageJ.</a> Biophotonics International. 11, 36-42 (2004).</li><li>Horiguchi, G., Fujikura, U., Ferjani, A., Ishikawa, N., Tsukaya, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+histological+analysis+of+leaf+mutants+using+two+simple+leaf+observation+methods:+identification+of+novel+genetic+pathways+governing+the+size+and+shape+of+leaves.">Large-scale histological analysis of leaf mutants using two simple leaf observation methods: identification of novel genetic pathways governing the size and shape of leaves.</a> Plant. J. 48, 638-644 (2006).</li><li>Horiguchi, G., Ferjani, A., Fujikura, U., Tsukaya, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coordination+of+cell+proliferation+and+cell+expansion+in+the+control+of+leaf+size+in+Arabidopsis+thaliana.">Coordination of cell proliferation and cell expansion in the control of leaf size in Arabidopsis thaliana.</a> J. Plant. Res. 119, 37-42 (2006).</li><li>Pierik, R., de Wit, M., Voesenek, L. A. C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth-mediated+stress+escape:+convergence+of+signal+transduction+pathways+activated+upon+exposure+to+two+different+environmental+stresses.">Growth-mediated stress escape: convergence of signal transduction pathways activated upon exposure to two different environmental stresses.</a> New. Phytol. 189, 122-134 (2011).</li></ol>

Aucun conflit d&#39;intérêt déclaré.

Notre &quot;LeafJ&quot; plugin permet de mesurer la longueur du pétiole semi-automatique, en augmentant le débit de près de 6 fois plus de mesure manuelle. Longueur du pétiole est un indice important de la SAS et est également un emblème d&#39;autres phénomènes, comme la résistance de submersion et la croissance hyponastic 17. Par conséquent, ce plugin peut être utile à un large éventail de chercheurs de plantes. Notre plugin est mis en œuvre dans un réseau bien ét...

<html><table border="1"><tbody><tr><td> Nom du réactif </td><td> Entreprise </td><td> Numéro de catalogue </td><td></td></tr><tr><td> rouge lointain lumière LED </td><td> Orbitec </td><td> sur mesure </td><td></td></tr><tr><td> transparence </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> Image 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> coutume </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

Phénotypage à haut débit (phénomique) est un outil puissant pour les liens entre les gènes de leurs fonctions (voir avis 1 et des exemples récents 2-4). Les feuilles sont l&#39;organe photosynthétique primaire, leur taille et leur forme varient du développement et de l&#39;environnement dans une usine. Pour ces raisons, les études sur la morphologie des feuilles nécessitent une mesure de plusieurs paramètres de nombreuses feuilles, qui est le mieux fait par des outils semi-automatiques Phenomics 5,6. Ombre Canopy est un indice important de l&#39;environnement qui affecte l&#39;architecture des plantes et de l&#39;histoire de vie, la suite des réponses est collectivement appelé le syndrome d&#39;évitement ombre (SAS) 7. Parmi les réponses SAS, ombre feuilles induit un allongement du pétiole et les changements de zone de la lame sont particulièrement utiles comme les indices 8. À ce jour, les programmes de la forme des feuilles (par exemple, forme 9, LAMINA 10, LeafAnalyzer 11, LEAFPROCESSOR 12) permet de mesurer les contours de feuilles et de catégoriser les formes de feuilles, Mais ne peut pas émettre la longueur du pétiole. Le manque de systèmes de mesure à grande échelle des pétioles des feuilles a inhibé les approches Phenomics à SAS de recherche. Dans cet article, nous décrivons un plugin ImageJ nouvellement développé, appelé LeafJ, qui peut rapidement mesurer la longueur du pétiole et limbe des paramètres de la plante modèle Arabidopsis thaliana. Pour la feuille de temps en temps que la correction manuelle requise de la frontière lame pétiole / feuille, nous avons utilisé une tablette à écran tactile. De plus, la forme des cellules des feuilles et le nombre de cellules des feuilles sont des déterminants importants de 13 la taille des feuilles. Séparer LeafJ nous présentons également un protocole d&#39;utilisation d&#39;une tablette à écran tactile pour mesurer la forme des cellules, la superficie et la taille. Notre système de mesure feuille de trait ne se limite pas à l&#39;ombre d&#39;évitement de recherche et permettra d&#39;accélérer le phénotypage feuille de mutants et de plantes de dépistage par phénotypage feuille.

1. Images Feuille Affichage estimations du pétiole et limbe frontière, et leur fenêtre de mesure L&#39;une des caractéristiques les plus utiles de LeafJ est la détection automatique des limbe / Pétiole limite (figure 1). L&#39;algorithme LeafJ fonctionne comme suit: le haut-ImageJ ParticleAnalyzer fonctionnalité est utilisée pour trouver et déterminer l&#39;orientation des feuilles à l&#39;intérieur de la sélection de l&#39;utilisateur. Pour chaque feuille de la lar...

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

Démonstration de méthodes de mesures clés pour la haute feuille de débit. Ces méthodes peuvent être utilisées pour accélérer le phénotypage feuille lors de l&#39;étude des mutants de nombreux végétaux ou installations de criblage autrement par le phénotype feuilles.

LeafJ: Un Plugin ImageJ pour semi-automatique de mesure Forme Feuille

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

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

Research

JoVE Journal

Biology

28.1K vues.  University of California Davis. Démonstration de méthodes de mesures clés pour la haute feuille de débit. Ces méthodes peuvent être utilisées pour accélérer le phénotypage feuille lors de l'étude des mutants de nombreux végétaux ou installations de criblage autrement par le phénotype feuilles.

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

Semi-automated Optical Heartbeat Analysis of Small Hearts

We have developed a method for analyzing high speed optical recordings from Drosophila, zebrafish and embryonic mouse hearts (Fink, et. al., 2009). Our Semi-automatic Optical Heartbeat Analysis (SOHA) uses a novel movement detection algorithm that is able to detect cardiac movements associated with individual contractile and relaxation events. The program provides a host of physiologically relevant readouts including systolic and diastolic intervals, heart rate, as well as qualitative and quantitative measures of heartbeat arrhythmicity. The program also calculates heart diameter measurements during both diastole and systole from which fractional shortening and fractional area changes are calculated. Output is provided as a digital file compatible with most spreadsheet programs. Measurements are made for every heartbeat in a record increasing the statistical power of the output. We demonstrate each of the steps where user input is required and show the application of our methodology to the analysis of heart function in all three genetically tractable heart models.

We have developed a Semi-automated Optical Heartbeat Analysis method (SOHA) for analyzing high speed optical recordings from Drosophila, zebrafish and embryonic mouse hearts. We demonstrate the application of our methodology to the analysis of heart function in fruit fly and embryonic mouse hearts.

Analyse semi-automatisée Heartbeat optique de petits coeurs

We have developed a method for analyzing high speed optical recordings from Drosophila, zebrafish and embryonic mouse hearts (Fink, et. al., 2009). Our ...

Recherche

Biologie

RNA Secondary Structure Prediction Using High-throughput SHAPE

Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed "high-throughput selective 2' hydroxyl acylation analyzed by primer extension", or SHAPE, allows prediction of RNA secondary structure with single nucleotide resolution. This approach utilizes chemical probing agents that preferentially acylate single stranded or flexible regions of RNA in aqueous solution. Sites of chemical modification are detected by reverse transcription of the modified RNA, and the products of this reaction are fractionated by automated capillary electrophoresis (CE). Since reverse transcriptase pauses at those RNA nucleotides modified by the SHAPE reagents, the resulting cDNA library indirectly maps those ribonucleotides that are single stranded in the context of the folded RNA. Using ShapeFinder software, the electropherograms produced by automated CE are processed and converted into nucleotide reactivity tables that are themselves converted into pseudo-energy constraints used in the RNAStructure (v5.3) prediction algorithm. The two-dimensional RNA structures obtained by combining SHAPE probing with in silico RNA secondary structure prediction have been found to be far more accurate than structures obtained using either method alone.

High-throughput selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) utilizes a novel chemical probing technology, reverse transcription, capillary electrophoresis and secondary structure prediction software to determine the structures of RNAs from several hundred to several thousand nucleotides at single nucleotide resolution.

ARN prédiction de la structure secondaire via SHAPE à haut débit

Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed ...

An Innovative Method for Exosome Quantification and Size Measurement

Although the biological importance of exosomes has recently gained an increasing amount of scientific and clinical attention, much is still unknown about their complex pathways, their bioavailability and their diverse functions in health and disease. Current work focuses on the presence and the behavior of exosomes (in vitro as well as in vivo) in the context of different human disorders, especially in the fields of oncology, gynecology and cardiology.
Unfortunately, neither a consensus regarding a gold standard for exosome isolation exists, nor is there an agreement on such a method for their quantitative analysis. As there are many methods for the purification of exosomes and also many possibilities for their quantitative and qualitative analysis, it is difficult to determine a combination of methods for the ideal approach. 
Here, we demonstrate nanoparticle tracking analysis (NTA), a semi-automated method for the characterization of exosomes after isolation from human plasma by ultracentrifugation. The presented results show that this approach for isolation, as well as the determination of the average number and size of exosomes, delivers reproducible and valid data, as confirmed by other methods, such as scanning electron microscopy (SEM).

A method for isolation of exosomes from whole blood and further analysis by nanoparticle tracking using a semi-automatic instrument is presented in this article. The presented technology provides an extremely sensitive method for visualizing and analyzing particles in liquid suspension.

Une méthode innovante pour Exosome Quantification et Taille Mesure

Although the biological importance of exosomes has recently gained an increasing amount of scientific and clinical attention, much is still unknown about ...

An Improved Method for Accurate and Rapid Measurement of Flight Performance in Drosophila

Drosophila has proven to be a useful model system for analysis of behavior, including flight. The initial flight tester involved dropping flies into an oil-coated graduated cylinder; landing height provided a measure of flight performance by assessing how far flies will fall before producing enough thrust to make contact with the wall of the cylinder. Here we describe an updated version of the flight tester with four major improvements. First, we added a &#34;drop tube&#34; to ensure that all flies enter the flight cylinder at a similar velocity between trials, eliminating variability between users. Second, we replaced the oil coating with removable plastic sheets coated in Tangle-Trap, an adhesive designed to capture live insects. Third, we use a longer cylinder to enable more accurate discrimination of flight ability. Fourth we use a digital camera and imaging software to automate the scoring of flight performance. These improvements allow for the rapid, quantitative assessment of flight behavior, useful for large datasets and large-scale genetic screens.

An Improved Method for Accurate and Rapid Measurement of Flight Performance in Drosophila

Here we describe a method for rapid and accurate measurement of flight performance in Drosophila, enabling high-throughput screening.

Une méthode améliorée pour la mesure précise et rapide des performances de vol en<em&gt; Drosophila</em

Drosophila has proven to be a useful model system for analysis of behavior, including flight. The initial flight tester involved dropping flies into an ...

Semi-automated Imaging of Tissue-specific Fluorescence in Zebrafish Embryos

Zebrafish embryos are a powerful tool for large-scale screening of small molecules. Transgenic zebrafish that express fluorescent reporter proteins are frequently used to identify chemicals that modulate gene expression. Chemical screens that assay fluorescence in live zebrafish often rely on expensive, specialized equipment for high content screening. We describe a procedure using a standard epifluorescence microscope with a motorized stage to automatically image zebrafish embryos and detect tissue-specific fluorescence. Using transgenic zebrafish that report estrogen receptor activity via expression of GFP, we developed a semi-automated procedure to screen for estrogen receptor ligands that activate the reporter in a tissue-specific manner. In this video we describe procedures for arraying zebrafish embryos at 24-48 hours post fertilization (hpf) in a 96-well plate and adding small molecules that bind estrogen receptors. At 72-96 hpf, images of each well from the entire plate are automatically collected and manually inspected for tissue-specific fluorescence. This protocol demonstrates the ability to detect estrogens that activate receptors in heart valves but not in liver.

Described here is a protocol for semi-automated imaging of tissue-specific fluorescence in zebrafish embryos.

Imagerie semi-automatique de la fluorescence spécifique de tissu dans embryons de poissons zèbres

Zebrafish embryos are a powerful tool for large-scale screening of small molecules. Transgenic zebrafish that express fluorescent reporter proteins are ...

Relating Stomatal Conductance to Leaf Functional Traits

Leaf functional traits are important because they reflect physiological functions, such as transpiration and carbon assimilation. In particular, morphological leaf traits have the potential to summarize plants strategies in terms of water use efficiency, growth pattern and nutrient use. The leaf economics spectrum (LES) is a recognized framework in functional plant ecology and reflects a gradient of increasing specific leaf area (SLA), leaf nitrogen, phosphorus and cation content, and decreasing leaf dry matter content (LDMC) and carbon nitrogen ratio (CN). The LES describes different strategies ranging from that of short-lived leaves with high photosynthetic capacity per leaf mass to long-lived leaves with low mass-based carbon assimilation rates. However, traits that are not included in the LES might provide additional information on the species&#39; physiology, such as those related to stomatal control. Protocols are presented for a wide range of leaf functional traits, including traits of the LES, but also traits that are independent of the LES. In particular, a new method is introduced that relates the plants&#8217; regulatory behavior in stomatal conductance to vapor pressure deficit. The resulting parameters of stomatal regulation can then be compared to the LES and other plant functional traits. The results show that functional leaf traits of the LES were also valid predictors for the parameters of stomatal regulation. For example, leaf carbon concentration was positively related to the vapor pressure deficit (vpd) at the point of inflection and the maximum of the conductance-vpd curve. However, traits that are not included in the LES added information in explaining parameters of stomatal control: the vpd at the point of inflection of the conductance-vpd curve was lower for species with higher stomatal density and higher stomatal index. Overall, stomata and vein traits were more powerful predictors for explaining stomatal regulation than traits used in the LES.

Unraveling how physiology and morphology are linked allows a deeper understanding of mechanistic functioning of plant leaves. We present both a procedure to derive parameters of stomatal regulation from stomatal conductance measurements and correlations with traditional functional leaf traits.

Concernant la conductance stomatique de feuilles traits fonctionnels

Leaf functional traits are important because they reflect physiological functions, such as transpiration and carbon assimilation. In particular, ...

Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins

The National Institute of Health&#39;s ImageJ is a powerful, freely available image processing software suite. ImageJ has comprehensive particle analysis algorithms which can be used effectively to count various biological particles. When counting large numbers of cell samples, the hemocytometer presents a bottleneck with regards to time. Likewise, counting membranes from migration/invasion assays with the ImageJ plugin Cell Counter, although accurate, is exceptionally labor intensive, subjective, and infamous for causing wrist pain. To address this need, we developed two plugins within ImageJ for the sole task of automated hemocytometer (or known volume) and migration/invasion cell counting. Both plugins rely on the ability to acquire high quality micrographs with minimal background. They are easy to use and optimized for quick counting and analysis of large sample sizes with built-in analysis tools to help calibration of counts. By combining the core principles of Cell Counter with an automated counting algorithm and post-counting analysis, this greatly increases the ease with which migration assays can be processed without any loss of accuracy.

This paper describes the quantification of hemocytometer and migration/invasion micrographs through two new open-source ImageJ plugins Cell Concentration Calculator and migration assay Counter. Furthermore, it describes image acquisition and calibration protocols as well as discusses in detail the input requirements of the plugins.

Automated Quantification et analyse des procédures de comptage cellulaire Utilisation ImageJ Plugins

The National Institute of Health&#39;s ImageJ is a powerful, freely available image processing software suite. ImageJ has comprehensive particle analysis ...

Clock Scan Protocol for Image Analysis: ImageJ Plugins

The clock scan protocol for image analysis is an efficient tool to quantify the average pixel intensity within, at the border, and outside (background) a closed or segmented convex-shaped region of interest, leading to the generation of an averaged integral radial pixel-intensity profile. This protocol was originally developed in 2006, as a visual basic 6 script, but as such, it had limited distribution. To address this problem and to join similar recent efforts by others, we converted the original clock scan protocol code into two Java-based plugins compatible with NIH-sponsored and freely available image analysis programs like ImageJ or Fiji ImageJ. Furthermore, these plugins have several new functions, further expanding the range of capabilities of the original protocol, such as analysis of multiple regions of interest and image stacks. The latter feature of the program is especially useful in applications in which it is important to determine changes related to time and location. Thus, the clock scan analysis of stacks of biological images may potentially be applied to spreading of Na+ or Ca++ within a single cell, as well as to the analysis of spreading activity (e.g., Ca++ waves) in populations of synaptically-connected or gap junction-coupled cells. Here, we describe these new clock scan plugins and show some examples of their applications in image analysis.

This paper describes two novel ImageJ plugins for &#39;Clock Scan&#39; image analysis. These plugins expand the functionality of the original visual basic 6 program and, most importantly, make the program available to a large research community by bundling it with the ImageJ free image analysis software package.

Protocole de numérisation de l&#39;horloge pour l&#39;analyse d&#39;image: Plugins ImageJ

The clock scan protocol for image analysis is an efficient tool to quantify the average pixel intensity within, at the border, and outside (background) a ...

Isolement semi-automatisé de tissu adipeux blanc murin

Semi-Automated Isolation of the Stromal Vascular Fraction from Murine White Adipose Tissue Using a Tissue Dissociator

The in vitro study of white, brown, and beige adipocyte differentiation enables the investigation of cell-autonomous functions of adipocytes and their mechanisms. Immortalized white preadipocyte cell lines are publicly available and widely used. However, the emergence of beige adipocytes in white adipose tissue in response to external cues is difficult to recapitulate to the full extent using publicly available white adipocyte cell lines. Isolation of the stromal vascular fraction (SVF) from murine adipose tissue is commonly executed to obtain primary preadipocytes and perform adipocyte differentiation. However, mincing and collagenase digestion of adipose tissue by hand can result in experimental variation and is prone to contamination. Here, we present a modified semi-automated protocol that utilizes a tissue dissociator for collagenase digestion to achieve easier isolation of the SVF, with the aim of reducing experimental variation, reducing contamination, and increasing reproducibility. The obtained preadipocytes and differentiated adipocytes can be used for functional and mechanistic analyses.

Pleins feux sur l’auteur : Isolement semi-automatisé de la fraction vasculaire stromale à partir de tissu adipeux blanc murin à l’aide d’un dissociateur tissulaire  

This protocol describes the semi-automated isolation of the stromal vascular fraction (SVF) from murine adipose tissue to obtain preadipocytes and achieve adipocyte differentiation in vitro. Using a tissue dissociator for collagenase digestion reduces experimental variation and increases reproducibility.

Isolement semi-automatisé de la fraction vasculaire stromale à partir de tissu adipeux blanc murin à l’aide d’un dissociateur tissulaire

The in vitro study of white, brown, and beige adipocyte differentiation enables the investigation of cell-autonomous functions of adipocytes and their ...