그는 글래드스톤 연구소에서 박사 캐서린 폴라드의 실험실에서 안식년에있는 동안 LeafJ는 JNM에 의해 작성되었습니다. 이 작품은 국립 과학 재단 (National Science Foundation) (교부금 번호 IOS-0923752)에서 교부금에 의해 지원되었다.

1. 식물 재료 이 식물의 성장 프로토콜이 커버 회피 응답을 검출하기위한 목적으로합니다. 니가 제일 좋아하는 조건에서 식물을 성장 할 수 있습니다. <ol><li> 어둠 속에서 4 일 동안 4에 9cm 페트리 요리와 저장소 (계 충화하다)를 ° C로 필터 종이를 흠뻑 물에 Arabidopsis thaliana의 씨앗을 뿌린다. </li><li> 모의 태양 조건에 해당 페트리 요리를 전송 : 1.86에 FR 비율 : 80-100 μE photosynthetically 활성화 방사선 (PAR)과 멀리 빨간 추가 요금이 부과 R을 가지고. 긴 하루를 조건 (16 시간 조명 / 8 시간 어두운) 및 (22)의 일정한 온도 ° C.를 사용하여 씨앗이 발아 할 수 있도록 3 일이 조건에 품다. </li><li> 토양에 germinated 씨앗을 전송, 일광욕 조건에서 식물을 유지. 대규모 실험, 우리는 레이블을 만들기위한 마이크로 소프트 워드 2004 (이상)에서 관리자를 병합 데이터를 사용하여 각 식물을 라벨에 작은 태그를 준비하는 것이 좋습니다. </li><li> 일레븐 일 TR 후토양에 ansfer는 그늘 상태에 식물의 절반을 이동 : 태양 있지만 0.52에 R / FR 비율을 가져다 보완 멀리 붉은 빛으로 동일합니다. </li><li> 추가 십이일 후, 식물 잎 이미지에 대한 준비가되어 있습니다. 당신은 개발의 스냅 샷을 캡처 할 수 있도록 어린 잎은 여전히​​ 확장하는 반면이 단계에서는 기존의 잎이 완전히 성숙했습니다. 당신은 당신의 요구에 따라 다른 발달 시간을 선택 할 수 있습니다. </li></ol> 2. 해부 잎 이미지 캡처 <ol><li> 다섯 직사각형 프레임이있는 식물 유전자형과 성장 조건과 함께 표시 투명 시트를 준비합니다. 한 프레임 한 공장에서 잎에 해당합니다. Microsoft Excel을이 레이블을 사용하여 일관된 그리드를 인쇄하는 데 사용할 수 있습니다. </li><li> 이십육일 오래된 식물의 잎을 해부. </li><li> 검사는 평면 침대 스캐너에서 600 DPI에서 출발합니다. 씨앗에서 출발 참고 투명 시트의 샌드위치에 검은 창에서 세로로 배치해야합니다. 감동 잎을 피다음 절차에 오류를 줄 것이다 검은 창 프레임과 중복 잎 있습니다. </li></ol> 3. LeafJ의 잎 이미지 분석 <ol><li> 다운로드 ImageJ ImageJ의 플러그인 폴더로 LeafJ.jar 파일을 드래그합니다. </li><li> ImageJ 1.45s 이상 14 이미지 파일을 엽니 다. </li><li> &quot;&gt; 분할 채널은 이미지&gt; 색상&quot;에 의해 3 색 채널 (빨강, 녹색, 파랑)로 이미지를 분할하고 파란색 채널의 이미지에 임계 값을 적용 할 수 있습니다. </li><li> 사각형 도구 (그림 1A)하여 한 공장에서 잎을 모두 선택합니다. </li><li> 플러그인 메뉴에서 &quot;LeafJ&quot;를 선택하십시오. </li><li> 나타나는 대화 상자에서이 공장 주석 정보를 선택하십시오. 당신은 할 수&quot;이러한 옵션 수정 &#39;을 클릭하여 여기에 표시되는 기본 값을 편집 할 수 있습니다. </li><li> LeafJ 플러그인을 실행 후에 &quot;OK&quot;버튼을 클릭하기 전에,이자 (ROI) 관리자 창 (, 그림 1B 필요한 경우)의 지역에서 추적 선을 편집 할 수 있습니다. 터치 스크린 태블릿 (예 : 아이 패드 등)이 절차에 유용합니다. iPads는 에어 디스플레이 소프트웨어를 사용하여 외부 모니터로 컴퓨터에 연결 할 수 있습니다. </li><li> 측정 결과 및 Microsoft Excel 또는 이에 상응하는 소프트웨어에 관련 정보 (파일 이름, 꽃 시간에 의해 해부에 의해 측정 등) 보냅니다. </li></ol> 4. ImageJ의 잎 세포 이미지 분석 <ol><li> 해부 해결은 (제 2 단계) 스캔 한 후 참조 15에 설명되어 출발합니다. FAA 고정 잎은 적어도 6 개월 이상에 대해 4 ° C에 보관하실 수 있습니다. </li><li> 현미경 관찰 15 전 1 ~ 2 시간에 클로 랄 하이드레이트 솔루션과 길러 잎에 FAA의 정착액을 변경하여 잎을 해제합니다. </li><li> 마운트 마일에 출발croscope는 trichomes가 직면과 슬라이드. trichomes 또는 정맥 근처의 세포를 피 주요 정맥의 양쪽에 각 잎의 중심 복합 현미경, 이미지 mesophyll 층에 40x 배율을 사용합니다. </li><li> 추적 잎 셀은 터치 스크린 태블릿과 스타일러스 (3 단계에서 설명한대로)의 도움을 ImageJ 투자 수익 (ROI) 관리자 도구에 의해 설명합니다. 세포 이미지 분석 ImageJ의 내장 된 기능을 사용하지만 LeafJ을 필요로하지 않습니다. </li></ol>

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관심 없음 충돌이 선언 없습니다.

우리의 &quot;LeafJ&quot;플러그인은 수동 측정을 통해 처리 할 거의 6 배 증가, 반 자동으로 잎자루 길이의 측정을 할 수 있습니다. 잎자루 길이는 SAS의 중요한 인덱스이며 또한 잠수 저항과 hyponastic 성장 17과 같은 다른 현상의 랜드 마크입니다. 따라서이 플러그인은 식물 연구자의 다양한 유용 할 수 있습니다. 우리 플러그인은 잘 알려진 자바 기반의 무료 소프트웨어, Im...

<html><table border="1"><tbody><tr><td> 시약의 이름 </td><td> 회사 </td><td> 카탈로그 번호 </td><td></td></tr><tr><td> 멀리 붉은 빛 LED </td><td> Orbitec </td><td> 사용자가 만든 </td><td></td></tr><tr><td> 투명도 </td><td> 상 </td><td> HSCA / 5 </td><td></td></tr><tr><td> 스캐너 </td><td> 엡손 </td><td> 엡손 완벽 V700 PHOTO </td><td></td></tr><tr><td> 이미지 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> 관습 </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> 에어 디스플레이 </td><td> Avatron 소프트웨어 주식회사 </td><td></td><td>빈 &quot;&gt; http://avatron.com/ </td></tr><tr><td> iPad2 </td><td> 애플 </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

높은 처리량 phenotyping (phenomics (주) 검토 1 최근 예 2-4 참조)의 기능과 유전자를 연결하기위한 강력한 도구입니다. 잎은 기본 광합성 기관이며, 크기와 모양이 공장 내에 발달 및 환경 다를 수 있습니다. 이러한 이유로 잎 형태에 대한 연구는 가장 반 자동화 phenomics 도구 5,6에 의해 수행됩니다 많은 잎에서 여러 매개 변수의 측정을 필요로합니다. 캐노피 그늘 공장 건축과 생활의 역사에 영향을 미치는 중요한 환경 큐, 응답의 스위트 룸은 총체적으로 그늘 회피 증후군 (SAS) 7이라고합니다. SAS 응답 중 그늘 유도 잎 잎자루의 신장 및 블레이드 지역의 변화는 인덱스 8과 같은 특히 유용합니다. 현재까지, 잎 모양 프로그램 (예 : SHAPE 9, 얇은 판 10, LeafAnalyzer 11 LEAFPROCESSOR 12) 잎 윤곽선을 측정하고 잎 모양을 분류 할 수 있습니다하지만 잎자루 길이를 출력 할 수 없습니다. 잎 petioles의 대규모 측정 시스템의 부족 SAS 연구 phenomics 방식을 저해하고 있습니다. 이 논문에서, 우리는 신속하게 모델 식물 Arabidopsis thaliana의의 잎자루 길이와 잎 블레이드 매개 변수를 측정 할 수 LeafJ라는 새로 개발 된 ImageJ 플러그인을, 설명합니다. 잎자루 / 잎 블레이드 경계의 필요한 수동 보정은 우리가 터치 스크린 태블릿을 사용하는 가끔 잎하십시오. 또한, 잎 세포 모양과 잎 셀 번호는 잎 크기로는 13의 중요한 determinants 있습니다. LeafJ는 별도로 우리는 또한 세포 모양, 면적 및 크기를 측정하기위한 터치 스크린 타블렛을 사용하는 프로토콜을 제시한다. 우리 잎의 특성 측정 시스템은 그늘 회피 연구에 한정되지 않고 잎 phenotyping에 의해 많은 돌연변이 검사 식물의 잎 phenotyping을 가속화합니다.

1. 잎자루과 리프 블레이드 경계의 견적보기 잎 이미지, 그리고 그들의 측정 창 LeafJ의 가장 유용한 기능 중 하나는 잎 블레이드 / 잎자루 경계 (그림 1)의 자동 감지합니다. 다음과 같이 LeafJ 알고리즘은 작동 내장 된 ImageJ ParticleAnalyzer 기능은 사용자 선택의 안쪽 잎의 방향을 찾아 결정하는 데 사용됩니다. 각 잎의 경우 잎의 폭은 잎의 전체 축을 따라 결정됩니다. 그...

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

높은 처리량 잎 측정을위한 주요 방법의 시범. 이러한 방법은 잎 표현형하여 많은 식물의 돌연변이 또는 기타 검사 식물을 공부할 때 잎 phenotyping을 가속화하는 데 사용할 수 있습니다.

LeafJ : 세미 자동 리프 형상 측정을위한 ImageJ 플러그인

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 조회수.  University of California Davis. 높은 처리량 잎 측정을위한 주요 방법의 시범. 이러한 방법은 잎 표현형하여 많은 식물의 돌연변이 또는 기타 검사 식물을 공부할 때 잎 phenotyping을 가속화하는 데 사용할 수 있습니다.

비디오: 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.

작은 하트의 세미 - 자동 광학 도면 분석

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

연구

생물학

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.

생활의 이미징 셀 모양 변경 Drosophila 태아

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.

높은 처리량 SHAPE를 사용하여 RNA 이차 구조 예측

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.

엑소 정량화 및 크기 측정을위한 혁신적인 방법

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.

비행 성능의 정확하고 빠른 측정을위한 개선 된 방법에<em&gt; 초파리</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.

Zebrafish의 태아의 조직 특이 형광의 반 자동화 이미징

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.

잎 기능 형질에 기공 컨덕턴스 관련된

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.

ImageJ에 플러그인을 사용하여 셀 카운팅 절차의 자동화 된 정량 및 분석

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.

이미지 분석을위한 클록 스캔 프로토콜 : 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 ...

murine white 지방 조직의 반자동 분리

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.

저자 스포트라이트: 조직 해리제를 사용하여 Murine White 지방 조직에서 기질 혈관 분획의 반자동 분리  

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.

조직 해리기를 사용하여 쥐 백색 지방 조직에서 기질 혈관 분획의 반자동 분리

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