LeafJ נכתב על ידי תל&quot;י בזמן שהוא היה בשנת השבתון במעבדתו של ד&quot;ר קתרין פולארד במכון גלדסטון. עבודה זו נתמכה על ידי מענק מהקרן הלאומי למדע (מענק מספר IOS-0923752).

1. חומרים צמחיים שים לב שפרוטוקול גידול צמחים שזה מכוון לאיתור תגובת הימנעות צל. ניתן לגדל צמחים בתנאים המועדפים עליך. <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> מפזרי זרעי thaliana ארבידופסיס על מים ספוגים ניירות סינון ב 9 מנות סנטימטר הפטר וחנויות (רבד) ב 4 ° C במשך ארבעה ימים בחושך. </li><li style=";text-align:right;direction:rtl"> להעביר צלחות פטרי אלה לתנאי יום ראשון מדומים: μE קרינת 80-100 photosynthetically פעילה (PAR) ותוספת מרחיקה אדומה להביא R: יחס FR ל1.86. השתמש בתנאי יום ארוכים (16 שעות אור / שעה אפלה 8) וטמפרטורה קבועה של 22 ° C. דגירה במצב זה במשך שלושה ימים על מנת לאפשר לזרעים לנבוט. </li><li style=";text-align:right;direction:rtl"> העברת הזרעים מונבטים לאדמה ולשמור על צמחים בתנאי יום ראשון לניסויים בקנה מידה גדול, אנו ממליצים להכין תגים קטנים לתיוג כל צמחים באמצעות מיזוג נתוני מנהל ב-Microsoft Word 2004 (או מאוחר יותר) להדפסת תוויות. </li><li style=";text-align:right;direction:rtl"> עשרה ימים לאחר transfer לאדמה, להעביר מחצית מהצמחים לתנאי צל: כמו שמש אבל עם אור משלים מרחיקה אדומה כדי להביא את יחס R / FR ל0.52. </li><li style=";text-align:right;direction:rtl"> לאחר 12 ימים נוספים, הצמחים מוכנים להדמית עלה. בשלב זה את העלים המבוגרים הבשילו באופן מלא ואילו עלים צעירים עדיין מתרחבים, כך שאתה ללכוד תמונת מצב של פיתוח. ייתכן שתרצה לבחור זמן התפתחותי שונה בהתאם לצרכימים שלך. </li></ol> 2. לכידת תמונות עלים גזורים <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> הכן גיליונות שקפים שכותרתו עם גנוטיפ צמח ומצב צמיחה עם חמש מסגרות מלבניות. מסגרת אחת מתאימה לעלים מצמח אחד. Microsoft Excel יכול לשמש להדפסת רשת בקנה אחד עם תוויות. </li><li style=";text-align:right;direction:rtl"> לנתח עלים של צמחים ישנים 26 יום. </li><li style=";text-align:right;direction:rtl"> הסריקה יוצאת ב600 dpi בסורק שטוח מיטה. שים לב שיוצא ממפעל אחד צריך להיות ממוקם אנכי בתוך חלון שחור בכריך של יריעות שקופות. הימנע מעלים נוגעיםלמסגרת שחורה חלון ועלים חופפים, אשר תיתנה לי טעויות בהליכים הבאים. </li></ol> 3. ניתוח תמונת עלה ידי LeafJ <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> ההורדה ImageJ גרור את קובץ LeafJ.jar לתוך תיקיית plugins של ImageJ. </li><li style=";text-align:right;direction:rtl"> פתח קובץ תמונה בImageJ 1.45s או במאוחר 14. </li><li style=";text-align:right;direction:rtl"> לפצל את התמונה לאפיקים השלושה צבעים (אדום, ירוק וכחול) על ידי &quot;תמונת צבע&gt;&gt; ערוצי Split&quot; ולהחיל סף לתמונה בערוץ הכחול. </li><li style=";text-align:right;direction:rtl"> בחר את כל העלים מצמח אחד על ידי כלי מלבן (איור 1 א). </li><li style=";text-align:right;direction:rtl"> בחר &quot;LeafJ&quot; מתפריט התוסף. </li><li style=";text-align:right;direction:rtl"> בחר מידע ליאור הצמח הזה מתיבת הדו השיח שמופיעה. אתה יכוללערוך את ערכי ברירת המחדל שמופיעים כאן על ידי לחיצה על &quot;ערוך אפשרויות אלה&quot;. </li><li style=";text-align:right;direction:rtl"> לאחר הפעלת תוסף LeafJ ולפני הלחיצה על כפתור &quot;אישור&quot;, לערוך לייחס קווים מאזור חלון עניין (ROI) מנהל (במידת צורך; 1B איור). לוח עם מסך מגע (כמו האייפד) שימושי להליך זה. אייפדים יכולים להיות מחוברים למחשב כצג חיצוני באמצעות תוכנת תצוגת אוויר. </li><li style=";text-align:right;direction:rtl"> יצוא תוצאות מדידה ומידע משויך (שמות קבצים, זמן פריחה, משופע ב, שנמדד על ידי, וכו &#39;) ל-Microsoft Excel או תוכנה מקבילה. </li></ol> 4. ניתוח תמונת תא עלה בImageJ <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> התקן גזור משאיר כמתואר ב15 התייחסות לאחר הסריקה (שלב 2). עלים קבועים FAA יכולים להיות כל זמן ב4 מעלות צלזיוס למשך 6 חודשים לפחות. </li><li style=";text-align:right;direction:rtl"> נקה את העלים על ידי שינוי מקבע-FAA לפתרון כלורל ועלי אינקובטורים ל1 ~ 2 שעות לפני התצפית מיקרוסקופית 15. </li><li style=";text-align:right;direction:rtl"> ההר משאיר במיילcroscope מחליק עם trichomes פונה כלפי מעלה. באמצעות הגדלת 40X במתחם מיקרוסקופ, תמונת שכבת mesophyll של מרכז כל עלה משני צדדיו של הווריד הראשי, הימנעות מתאים הסמוכים trichomes או ורידים. </li><li style=";text-align:right;direction:rtl"> תא עלה עקבות מתאר ידי כלי מנהל ROI ImageJ עם סיוע של לוח עם מסך מגע וסטיילוס (כמתואר בשלב 3). ניתוח תמונת תא משתמש בתכונות המוכללות של ImageJ אך אינו מחייב LeafJ. </li></ol>

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אין ניגודי האינטרסים הכריזו.

התוסף שלנו &quot;LeafJ&quot; מאפשר מדידת אורך פטוטרת חצי אוטומטית, הגדלת תפוקה כמעט 6 פעמים במדידה ידנית. אורך פטוטרת הוא מדד חשוב של SAS וגם לציון דרך של תופעות אחרות, כגון התנגדות שקיעה וצמיחת hyponastic 17. לכן תוסף זה יכול להיות שימושי למגוון רחב של חוקרי צמחים. <p class="jove_conte...

<html><table border="1" style=";text-align:right;direction:rtl"><tbody><tr><td> שם המגיב </td><td> חברה </td><td> מספר קטלוגים </td><td></td></tr><tr><td> אור מרחיק נורית אדומה </td><td> Orbitec </td><td> המנהג עשה </td><td></td></tr><tr><td> שקיפות </td><td> אייקון </td><td> HSCA / 5 </td><td></td></tr><tr><td> סורק </td><td> Epson </td><td> Epson Perfection V700 PHOTO </td><td></td></tr><tr><td> התמונה 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> מנהג </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> אוויר תצוגה </td><td> Avatron תוכנה בע&quot;מ </td><td></td><td>ריק &quot;&gt; http://avatron.com/ </td></tr><tr><td> iPad2 </td><td> אפל </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

phenotyping תפוקה הגבוהה (Phenomics) הוא כלי רב עצמה לקישור גנים לתפקידם (ראה 1 ביקורת והדוגמות אחרונות 2-4). עלים הם איבר הפוטוסינתזה הראשוני, והגודל וצורתם משתנים התפתחותית והסביבה בתוך מפעל. מסיבות אלה מחקרים על מורפולוגיה עלה דורשים מדידה של מספר פרמטרים מעלים רבים, שנעשה על ידי מיטב כלים אוטומטיים למחצה Phenomics 5,6. צל חופה הוא רמז סביבתי חשוב שמשפיע על אדריכלות מפעל ותולדות חיים; החבילה של תגובות נקראת באופן קולקטיבי תסמונת הימנעות הצל (SAS) 7. בין תגובות SAS, התארכות צל מושרה עלה פטוטרת ושינויים באזור הלהב הם שימושיים במיוחד כמדדי 8. נכון להיום, תוכניות צורת עלים (למשל SHAPE 9, Lamina 10, 11 LeafAnalyzer, LEAFPROCESSOR 12) יכולות למדוד את קווי מתאר עלים ולמיין צורות עלים, אבל לא יכול פלט אורך פטוטרת. חוסר מערכות מדידה בקנה מידה הגדולה של פטוטרות עלה יש עכבות גישות Phenomics לSAS מחקר. במאמר זה, אנו מתארים תוסף חדש שפותח ImageJ, נקרא LeafJ, שמהירות יכול למדוד אורך פטוטרת ופרמטרי להב עלה של צמח המודל ארבידופסיס thaliana. לעלה מזדמן שתיקון ידני הנדרש של גבול להב הפטוטרת / עלה הייתי לוח עם מסך מגע. יתר על כן, צורת תא עלה ומספרים סלולריים עלים הם גורמים חשובים בגודל העלה 13. נפרד מLeafJ אנחנו גם מציגים פרוטוקול לשימוש במחשב לוח עם מסך מגע למדידת צורת תא, שטח וגודל. מערכת מדידת תכונת עלנו אינה מוגבלת למחקר צל, הימנעות ותאיץ phenotyping עלה של מוטציות רבות וצמחים על ידי הקרנת phenotyping עלה.

1. תמונות עלים מציגים אומדני הפטוטרת וגבול להב עלה, ועל חלון המדידה שלהם אחת התכונות השימושיות ביותר של LeafJ הוא זיהוי אוטומטי של גבול להב / פטוטרת עלה (איור 1). אלגוריתם LeafJ עובד כדלקמן: הפונקציונליות המובנית ParticleAnalyzer ImageJ משמ?...

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

הדגמה של שיטות עיקריות למדידה עלתה תפוקה גבוהה. שיטות אלה יכולים לשמש כדי להאיץ phenotyping עלה כאשר לומדים הרבה מוטנטים צמחיים או אחר על ידי צמחי הקרנה פנוטיפ עלה.

LeafJ: תוסף ImageJ למדידת צורת עלה חצי אוטומטית

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 Views.  University of California Davis. הדגמה של שיטות עיקריות למדידה עלתה תפוקה גבוהה. שיטות אלה יכולים לשמש כדי להאיץ phenotyping עלה כאשר לומדים הרבה מוטנטים צמחיים או אחר על ידי צמחי הקרנה פנוטיפ עלה.

Video: 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.

חצי אוטומטיות Heartbeat ניתוח אופטי של לבבות קטנים

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

Imaging Cell Shape Change in Living Drosophila Embryos

The developing Drosophila melanogaster embryo undergoes a number of cell shape changes that are highly amenable to live confocal imaging. Cell shape changes in the fly are analogous to those in higher organisms, and they drive tissue morphogenesis. So, in many cases, their study has direct implications for understanding human disease (Table 1)1-5. On the sub-cellular scale, these cell shape changes are the product of activities ranging from gene expression to signal transduction, cell polarity, cytoskeletal remodeling and membrane trafficking. Thus, the Drosophila embryo provides not only the context to evaluate cell shape changes as they relate to tissue morphogenesis, but also offers a completely physiological environment to study the sub-cellular activities that shape cells.
The protocol described here is designed to image a specific cell shape change called cellularization. Cellularization is a process of dramatic plasma membrane growth, and it ultimately converts the syncytial embryo into the cellular blastoderm. That is, at interphase of mitotic cycle 14, the plasma membrane simultaneously invaginates around each of ~6000 cortically anchored nuclei to generate a sheet of primary epithelial cells. Counter to previous suggestions, cellularization is not driven by Myosin-2 contractility6, but is instead fueled largely by exocytosis of membrane from internal stores7. Thus, cellularization is an excellent system for studying membrane trafficking during cell shape changes that require plasma membrane invagination or expansion, such as cytokinesis or transverse-tubule (T-tubule) morphogenesis in muscle.
Note that this protocol is easily applied to the imaging of other cell shape changes in the fly embryo, and only requires slight adaptations such as changing the stage of embryo collection, or using "embryo glue" to mount the embryo in a specific orientation (Table 1)8-19. In all cases, the workflow is basically the same (Figure 1). Standard methods for cloning and Drosophila transgenesis are used to prepare stable fly stocks that express a protein of interest, fused to Green Fluorescent Protein (GFP) or its variants, and these flies provide a renewable source of embryos. Alternatively, fluorescent proteins/probes are directly introduced into fly embryos via straightforward micro-injection techniques9-10. Then, depending on the developmental event and cell shape change to be imaged, embryos are collected and staged by morphology on a dissecting microscope, and finally positioned and mounted for time-lapse imaging on a confocal microscope.

Imaging Cell Shape Change in Living Drosophila Embryos

Early development of the fruit fly, Drosophila melanogaster, is characterized by a number of cell shape changes that are well suited for imaging approaches. This article will describe basic tools and methods required for live confocal imaging of Drosophila embryos, and will focus on a cell shape change called cellularization.

צורה הדמיה תא שינוי חיים תסיסנית עוברים

The developing Drosophila melanogaster embryo undergoes a number of cell shape changes that are highly amenable to live confocal imaging.  Cell shape ...

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.

חיזוי מבנה המשני RNA באמצעות SHAPE תפוקה גבוהה

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.

שיטה חדשנית לExosome כימות ומדידה גודל

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.

שיטה משופרת למדידה מדויקת והמהירה של טיסה בביצועים<em&gt; דרוזופילה</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.

הדמיה חצי אוטומטית של הקרינה רקמות ספציפיות בעוברי דג הזברה

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.

הנוגע לתכונות מוליכות הפיוניות פונקציונליות ליף

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.

כימותים אוטומטיים וניתוח הליכי ספירה הניידת באמצעות תוספי ImageJ

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.

שעון סריקה פרוטוקול ניתוח תמונה: 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 ...

בידוד חצי אוטומטי של רקמת שומן לבנה מורין

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.

מחבר זרקור: בידוד חצי אוטומטי של מקטע כלי הדם סטרומה מרקמת שומן לבן מורין באמצעות דיסוציאטור רקמות  

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.

בידוד חצי אוטומטי של מקטע כלי הדם הסטרומלי מרקמת השומן הלבנה באמצעות דיסוציאטור רקמות

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