Besonderer Dank geht an Cori Sanders bei Iroc Designs zur Vorbereitung von Illustrationen und Kris Reddi an der UCLA für die Einrichtung Probe Kulturen für Zahlen. Finanzierung für dieses Projekt wurde von HHMI (HHMI Grant Nr. 52006944) zur Verfügung gestellt.

<ol>
	<li>Barker, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> At the Bench: A Laboratory Navigator. , (1998).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Biosafety in Microbiological And Biomedical Laboratories (BMBL). , (2009).</li><li>Bykowski, T., Stevenson, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aseptic+Technique.">Aseptic Technique.</a> Current Protocols in Microbiology. Appendix 4, Appendix 4D (2008).</li><li>Cot&#233;, R. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aseptic+Technique+for+Cell+Culture.">Aseptic Technique for Cell Culture.</a> Current Protocols in Cell Biology. Chapter 1, Unit 1.3 (2001).</li><li>Grimes, S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+basic+laboratory+manual+for+the+small-scale+production+and+testing+of+I-2+Newcastle+disease+vaccine.">A basic laboratory manual for the small-scale production and testing of I-2 Newcastle disease vaccine.</a> RAP Publication. AC802/E, 12-13 (2002).</li><li>Guzman, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pipetting:+A+Practical+Guide.">Pipetting: A Practical Guide.</a> The American Biology Teacher. 63 (2), 128-131 (2001).</li><li>Jordan, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> RESEARCH: National Genomics Research Initiative Phage Resource Laboratory Manual. , (2008).</li><li>Sambrook, J., Russell, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Molecular Cloning - A Laboratory Manual. , 978-087969576 (2001).</li><li>Seidman, L. A., Moore, 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=.">.</a> Basic Laboratory Methods for Biotechnology: Textbook and Laboratory Reference. , (2000).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> PIPETMAN P User's Guide. , (2012).</li></ol>

Ich habe nichts zu offenbaren.

Aseptische Technik bezieht sich auf eine Reihe von Routine-Verfahren erfolgen, um sterile Lösungen und Kulturen kontaminiert werden durch unerwünschte Mikroorganismen im Labor zu verhindern. Solche Techniken sind für Experimente, die wachsenden Zellen erfordern. Obwohl ein Werk-Einstellung, die völlig steril ist, kann nicht erreicht werden, dass Verfahren wie desinfizierende Oberflächen im Labor, die Schaffung eines sterilen Bereich mit einem Bunsenbrenner, die Begrenzung der Exposition der nicht begrenzten Kulturen und Medien an der Luft, Sterilisieren Materialien wie Flaschen, Tuben und Glaspipetten, und die Vermeidung von Kontakt von sterilen Instrumenten mit nicht-sterilen Oberflächen verringert die Möglichkeit einer Kontaminierung Lösungen und Kulturen in einem Experiment. Das Ziel ist, für diese vorsorgliche Verfahren zur zweiten Natur werden, dies wird mit Ausbildung und Praxis während der Arbeit in einem Labor. Volume Transfers mit sterilen Lösungen und Kulturen mit Instrumenten wie serologischen Pipetten und Mikrofonropipettors sind eine von vielen Arten von Routinetechniken in einem Labor durchgeführt. Verschiedene experimentelle Anwendungen erfordern Instrumente übertragen kann eigenständig, aber präzise und genau, Bände. Serologische Pipetten werden in mikrobiologischen Laboratorien verwendet werden, um Zellkulturen erfordern Medien Vorbereitungen beteiligt Milliliter Volumen vorzubereiten, während Mikroliterpipetten unbedingt molekularbiologische Experimente, die nur Mikroliter-Mengen von Lösungen benötigen. Wenn aseptischen Bedingungen mit diesen Instrumenten ausgeübt wird, wird Verunreinigung während Volumen Übertragungen unabhängig von der Höhe der Flüssigkeit oder Art von Experiment minimiert. Obwohl es in diesem Protokoll beschrieben, ist ein weiteres Mittel häufig verwendet, um eine Kontamination zu verhindern in einer Sterilbank (10) arbeiten. Diese Ausrüstung ist entscheidend für Gewebekulturen und für Experimente mit Mikroorganismen wie BLS-2 oder höher eingestuft durchgeführt. Ein Laminarströmungshaube enthält einen HEPA (high-efficiencyParticulate Air)-Filter, der Verunreinigungen aus der Luft entfernt von der strömenden Luft in die Haube und verhindert gleichzeitig ungefilterte Luft aus dem Raum durchdringt den Arbeitsbereich aus. Zu beachten ist, kann ein Bunsenbrenner nicht in einer Sterilbank verwendet werden, da die Wärme von der Flamme stört Luftstrom wesentlich für die Funktion der Haube. Es ist oft hilfreich, um die Qualität Ihrer aseptischen Bedingungen zu überprüfen, wenn die Durchführung von Experimenten. Um Lösungen zu bestätigen und Kulturmedien nicht während experimentelle Manipulationen verunreinigt, stets einen negativen Kontrolle. Zum Beispiel, wenn Herstellung Röhren-Bouillon für das Wachstum von Bakterienkulturen, nicht zu inokulieren ein Rohr so ​​dass nur sterile Medien. Inkubieren Sie das Medium neben den inokulierten Röhrchen dann inspizieren inokulierten Kontrolle Rohr auf Anzeichen von Kontamination wie Trübung von Wachstum unerwünschter Zellen unbeabsichtigt in das Rohr eingeführt. Wenn das Steuerrohr verunreinigt ist, die Versuchsröhres wahrscheinlich ist es, wie auch, kontaminiert und das Experiment muss wiederholt werden. Diese Vorsicht sollte bei jedem Experiment durchgeführt werden.

<table border="1"><tbody><tr><td> Name des Reagenzes </td><td> Firma </td><td> Katalog-Nummer </td><td> Kommentare </td></tr><tr><td> LB-Nährlösung </td><td> Difco </td><td> 244620 </td><td> Rezept auch in Referenz 6 </td></tr><tr><td colspan="4"> TE-Puffer: </td></tr><tr><td> EDTA Dinatriumsalz Dihydrat </td><td> Sigma </td><td> E5134 </td><td></td></tr><tr><td> Trizma-HCl </td><td> Sigma </td><td> T-3253 </td><td></td></tr><tr><td> CiDecon </td><td> Decon Laboratories, Inc. </td><td> 8504 </td><td> Desinfektionsmittel </td></tr><tr><td> Ethanol </td><td> Fisher Scientific </td><td> A406 </td><td> Für die Verwendung als Desinfektionsmittel, bereiten 70% (v / v) mit destilliertem Wasser </td></tr></tbody></table>

aseptic laboratory techniques: volume transfers with serological pipettes and micropipettors

Mikroorganismen sind überall - in der Luft, des Bodens und menschlichen Körper als auch auf unbelebten Oberflächen wie Labortische und Computer-Tastaturen. Die weite Verbreitung von Mikroben erzeugt eine reichliche Menge von möglichen Verunreinigungen in einem Labor. Um experimentelle Erfolg zu gewährleisten, muss die Zahl der Verunreinigungen an Geräten und Arbeitsflächen minimiert werden. Gemeinsame unter vielen Experimenten in der Mikrobiologie sind Techniken, bei denen die Messung und Übertragung von Kulturen mit bakteriellen Zellen oder Viruspartikeln. Um dies tun, ohne Kontakt mit unsterilen Oberflächen oder verunreinigen sterilen Medien erfordert (1) Herstellung einer sterilen Arbeitsbereich (2) eine exakte Einstellung und genau liest Instrumente für die aseptische Transfer von Flüssigkeiten, und (3) richtig zu manipulieren Instrumente, Kulturen Flakons, Flaschen und Rohre in einem sterilen Bereich. Lernen Sie diese Verfahren ruft für Ausbildung und Praxis. Zunächst sollten die Maßnahmen nur langsam, bedächtig und kontrolliert mit dem Ziel einer für die aseptische technik zur zweiten Natur werden bei der Arbeit an der Werkbank. Hier präsentieren wir Ihnen die Schritte zur Messung von Volumes mit serologischen Pipetten und Mikroliterpipetten in einem sterilen Bereich durch einen Bunsenbrenner erstellt. Volumenbereich von Mikroliter (ul) bis Milliliter (ml) je nach Instrument eingesetzt. Flüssigkeiten im Allgemeinen übertragen gehören steriler Bouillon oder chemische Lösungen sowie bakterielle Kulturen und Phagen-Aktien. Durch die folgenden Verfahren sollen die Studierenden in der Lage: <ul><li> Die Arbeiten innerhalb des sterilen Feldes durch die Bunsenbrennerflamme erstellt. </li><li> Verwenden Sie serologischen Pipetten, ohne Sterilität der Instrumente. </li><li> Absaugen von Flüssigkeiten mit serologischen Pipetten, genau zu lesen kalibrierten Volumina durch Ausrichten des Meniskus durch die Flüssigkeit zu den Teilstrichen auf der Pipette gebildet. </li><li> Halten Kultur Flaschen, Flakons, Tuben und ihrer jeweiligen Caps sterile Flüssigkeit während des Transfers. </li><li> Identifizieren verschiedene Anwendungen für Kunststoff gegenüber Glas serologische pipEttes. </li><li> Staatliche Grenzen für Genauigkeit Mikroliterpipetten. </li><li> Präzise und genau eingestellt Volumes auf Mikroliterpipetten. </li><li> Wissen, wie man richtig mit dem ersten und zweiten Station auf einer Mikropipette zum Ansaugen und übertragen richtige Bände. </li></ul>

Watch this Scientific Journal Video about Aseptic Laboratory Techniques: Volume Transfers with Serological Pipettes and Micropipettors at JoVE.com

Aseptic Laboratory Techniques: Volume Transfers with Serological Pipettes and Micropipettors

Bei der Arbeit in einem Labor, ist es zwingend notwendig, um Quellen der Kontamination zu minimieren. Aseptische Technik bezieht sich auf Verfahren, die Übertragung von Kulturen und Reagenzien ermöglichen, während der Kontakt mit nicht-sterilen Oberflächen. Serologische Pipetten und Mikroliterpipetten werden verwendet, um genaue Volumen, ohne dabei die Sterilität der Lösungen in Versuchen verwendet zu messen.

Aseptische Labortechnik: Volume Transfers mit serologischen Pipetten und Mikropipetten

Microorganisms are everywhere - in the air, soil, and human body as well as on inanimate surfaces like laboratory benches and computer keyboards. The ...

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161.8K Aufrufe.  University of California, Los Angeles. Bei der Arbeit in einem Labor, ist es zwingend notwendig, um Quellen der Kontamination zu minimieren. Aseptische Technik bezieht sich auf Verfahren, die Übertragung von Kulturen und Reagenzien ermöglichen, während der Kontakt mit nicht-sterilen Oberflächen. Serologische Pipetten und Mikroliterpipetten werden verwendet, um genaue Volumen, ohne dabei die Sterilität der Lösungen in Versuchen verwendet zu messen.

Serie: Aseptic Laboratory Techniques: Volume Transfers with Serological Pipettes and Micropipettors

Microbial Communities in Nature and Laboratory - Interview

Mikrobielle Gemeinschaften in Natur und Labor - Interview

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Biologie

Making Patch-pipettes and Sharp Electrodes with a Programmable Puller

Glass microelectrodes (also called pipettes) have been a workhorse of electrophysiology for decades. Today, such pipettes are made from glass capillaries using a programmable puller. Such instruments heat the capillary using either a metal filament or a laser and draw out the glass using gravity, a motor or both. Pipettes for patch-clamp recording are formed using only heat and gravity, while sharp electrodes for intracellular recording use a combination of heat, gravity, and a motor. The procedure used to make intracellular recording pipettes is similar to that used to make injection needles for a variety of applications, including cRNA injection into Xenopus oocytes. In general, capillary glass &lt;1.2 mm in diameter is used to make pipettes for patch clamp recording, while narrower glass is used for intracellular recording (outer diameter = 1.0 mm). For each tool, the puller is programmed slightly differently. This video shows how to make both kinds of recording pipettes using pre-established puller programs.

This video shows how to use a programmable puller to make patch pipettes and sharp electrodes for electrophysiology. The same procedure can be used to make a variety of glass tools, including injection needles.

Machen Patch-Pipetten und Sharp Elektroden mit einem programmierbaren Puller

Glass microelectrodes (also called pipettes) have been a workhorse of electrophysiology for decades.  Today, such pipettes are made from glass capillaries ...

Pressure-polishing Pipettes for Improved Patch-clamp Recording

Pressure-polishing is a method for shaping glass pipettes for patch-clamp recording. We first developed this method for fabricating pipettes suitable for recording from small (&lt;3 m) neuronal cell bodies. The basic principal is similar to glass-blowing and combines air pressure and heat to modify the shape of patch pipettes prepared by a conventional micropipette puller. It can be applied to so-called soft (soda lime) and hard (borosilicate) glasses. Generally speaking, pressure polishing can reduce pipette resistance by 25% without decreasing the diameter of the tip opening (Goodman and Lockery, 2000). It can be applied to virtually any type of glass and requires only the addition of a high-pressure valve and fitting to a microforge. This technique is essential for recording from ultrasmall cells (&lt;5 m) and can also improve single-channel recording by minimizing pipette resistance. The blunt shape is also useful for perforated-patch clamp recording since this tip shape results in a larger membrane bleb available for perforation.

This is a guide to modifying the shape of glass micropipettes. Specifically, by using heat and air pressure the taper is widened without increasing the tip opening, leading to lower pipette resistance. This is critical to obtain low noise recordings of small cells but is useful in many applications.

Pressure-Polieren Pipetten für verbesserte Patch-Clamp Recording

Pressure-polishing is a method for shaping glass pipettes for patch-clamp recording.  We first developed this method for fabricating pipettes suitable for ...

Modeling Biological Membranes with Circuit Boards and Measuring Electrical Signals in Axons: Student Laboratory Exercises

This is a demonstration of how electrical models can be used to characterize biological membranes. This exercise also introduces biophysical terminology used in electrophysiology. The same equipment is used in the membrane model as on live preparations. Some properties of an isolated nerve cord are investigated: nerve action potentials, recruitment of neurons, and responsiveness of the nerve cord to environmental factors.

This is a demonstration of how biological membranes can be understood using electrical models. We also demonstrate procedures for recording action potentials from the ventral nerve cord of the crayfish for student orientated laboratories.

Modellierung biologischer Membranen mit Leiterplatten und Messung elektrischer Signale in Axone: Schülerlabor Übungen

This is a demonstration of how electrical models can be used to characterize biological membranes. This exercise also introduces biophysical terminology ...

Aseptic Laboratory Techniques: Plating Methods

Microorganisms are present on all inanimate surfaces creating ubiquitous sources of possible contamination in the laboratory. Experimental success relies on the ability of a scientist to sterilize work surfaces and equipment as well as prevent contact of sterile instruments and solutions with non-sterile surfaces. Here we present the steps for several plating methods routinely used in the laboratory to isolate, propagate, or enumerate microorganisms such as bacteria and phage. All five methods incorporate aseptic technique, or procedures that maintain the sterility of experimental materials. Procedures described include (1) streak-plating bacterial cultures to isolate single colonies, (2) pour-plating and (3) spread-plating to enumerate viable bacterial colonies, (4) soft agar overlays to isolate phage and enumerate plaques, and (5) replica-plating to transfer cells from one plate to another in an identical spatial pattern. These procedures can be performed at the laboratory bench, provided they involve non-pathogenic strains of microorganisms (Biosafety Level 1, BSL-1). If working with BSL-2 organisms, then these manipulations must take place in a biosafety cabinet. Consult the most current edition of the Biosafety in Microbiological and Biomedical Laboratories (BMBL) as well as Material Safety Data Sheets (MSDS) for Infectious Substances to determine the biohazard classification as well as the safety precautions and containment facilities required for the microorganism in question. Bacterial strains and phage stocks can be obtained from research investigators, companies, and collections maintained by particular organizations such as the American Type Culture Collection (ATCC). It is recommended that non-pathogenic strains be used when learning the various plating methods. By following the procedures described in this protocol, students should be able to: 
 
&#9679; Perform plating procedures without contaminating media. 
&#9679; Isolate single bacterial colonies by the streak-plating method. 
&#9679; Use pour-plating and spread-plating methods to determine the concentration of bacteria. 
&#9679; Perform soft agar overlays when working with phage. 
&#9679; Transfer bacterial cells from one plate to another using the replica-plating procedure. 
&#9679; Given an experimental task, select the appropriate plating method.

When working with media and reagents used to culture microorganisms, aseptic technique must be practiced to ensure contamination is minimized. A variety of plating methods are routinely used to isolate, propagate, or enumerate bacteria and phage, all of which incorporate procedures that maintain the sterility of experimental materials.

Aseptische Labortechnik: Überzug Methoden

Microorganisms are present on all inanimate surfaces creating ubiquitous sources of possible contamination in the laboratory. Experimental success relies ...

Reconstruction of 3-Dimensional Histology Volume and its Application to Study Mouse Mammary Glands

Histology volume reconstruction facilitates the study of 3D shape and volume change of an organ at the level of macrostructures made up of cells. It can also be used to investigate and validate novel techniques and algorithms in volumetric medical imaging and therapies. Creating 3D high-resolution atlases of different organs1,2,3 is another application of histology volume reconstruction. This provides a resource for investigating tissue structures and the spatial relationship between various cellular features. We present an image registration approach for histology volume reconstruction, which uses a set of optical blockface images. The reconstructed histology volume represents a reliable shape of the processed specimen with no propagated post-processing registration error. The Hematoxylin and Eosin (H&#38;E) stained sections of two mouse mammary glands were registered to their corresponding blockface images using boundary points extracted from the edges of the specimen in histology and blockface images. The accuracy of the registration was visually evaluated. The alignment of the macrostructures of the mammary glands was also visually assessed at high resolution.
This study delineates the different steps of this image registration pipeline, ranging from excision of the mammary gland through to 3D histology volume reconstruction. While 2D histology images reveal the structural differences between pairs of sections, 3D histology volume provides the ability to visualize the differences in shape and volume of the mammary glands.

We present an image registration approach for 3-dimensional (3D) histology volume reconstruction, which facilitates the study of the changes of an organ at the level of macrostructures made up of cells . Using this approach, we studied the 3D changes between wild-type and Igfbp7-null mammary glands.

Die Rekonstruktion der 3-Dimensional Histologie Volume und seine Anwendung auf Maus Milchdrüsen Studieren

Histology volume reconstruction facilitates the study of 3D shape and volume change of an organ at the level of macrostructures made up of cells. It can ...

Techniques for the Analysis of Extracellular Vesicles Using Flow Cytometry

Extracellular Vesicles (EVs) are small, membrane-derived vesicles found in bodily fluids that are highly involved in cell-cell communication and help regulate a diverse range of biological processes. Analysis of EVs using flow cytometry (FCM) has been notoriously difficult due to their small size and lack of discrete populations positive for markers of interest. Methods for EV analysis, while considerably improved over the last decade, are still a work in progress. Unfortunately, there is no one-size-fits-all protocol, and several aspects must be considered when determining the most appropriate method to use. Presented here are several different techniques for processing EVs and two protocols for analyzing EVs using either individual detection or a bead-based approach. The methods described here will assist with eliminating the antibody aggregates commonly found in commercial preparations, increasing signal&#8211;to-noise ratio, and setting gates in a rational fashion that minimizes detection of background fluorescence. The first protocol uses an individual detection method that is especially well suited for analyzing a high volume of clinical samples, while the second protocol uses a bead-based approach to capture and detect smaller EVs and exosomes.

Many different methods exist for the measurement of extracellular vesicles (EVs) using flow cytometry (FCM). Several aspects should be considered when determining the most appropriate method to use. Two protocols for measuring EVs are presented, using either individual detection or a bead-based approach.

Techniken für die Analyse der extrazellulären Vesikeln mittels Durchflusszytometrie

Extracellular Vesicles (EVs) are small, membrane-derived vesicles found in bodily fluids that are highly involved in cell-cell communication and help ...

Measuring Pressure Volume Loops in the Mouse

Understanding the causes and progression of heart disease presents a significant challenge to the biomedical community. The genetic flexibility of the mouse provides great potential to explore cardiac function at the molecular level. The mouse&#39;s small size does present some challenges in regards to performing detailed cardiac phenotyping. Miniaturization and other advancements in technology have made many methods of cardiac assessment possible in the mouse. Of these, the simultaneous collection of pressure and volume data provides a detailed picture of cardiac function that is not available through any other modality. Here a detailed procedure for the collection of pressure-volume loop data is described. Included is a discussion of the principles underlying the measurements and the potential sources of error. Anesthetic management and surgical approaches are discussed in great detail as they are both critical to obtaining high quality hemodynamic measurements. The principles of hemodynamic protocol development and relevant aspects of data analysis are also addressed.

This manuscript describes a detailed protocol for the collection of pressure-volume data from the mouse.

Mess Druck Volumen Loops in der Maus

Understanding the causes and progression of heart disease presents a significant challenge to the biomedical community. The genetic flexibility of the ...

Techniques to Induce and Quantify Cellular Senescence

In response to cellular stress or damage, proliferating cells can induce a specific program that initiates a state of long-term cell-cycle arrest, termed cellular senescence. Accumulation of senescent cells occurs with organismal aging and through continual culturing in vitro. Senescent cells influence many biological processes, including embryonic development, tissue repair and regeneration, tumor suppression, and aging. Hallmarks of senescent cells include, but are not limited to, increased senescence-associated &#946;-galactosidase activity (SA-&#946;-gal); p16INK4A, p53, and p21 levels; higher levels of DNA damage, including &#947;-H2AX; the formation of Senescence-associated Heterochromatin Foci (SAHF); and the acquisition of a Senescence-associated Secretory Phenotype (SASP), a phenomenon characterized by the secretion of a number of pro-inflammatory cytokines and signaling molecules. Here, we describe protocols for both replicative and DNA damage-induced senescence in cultured cells. In addition, we highlight techniques to monitor the senescent phenotype using several senescence-associated markers, including SA-&#946;-gal, &#947;-H2AX and SAHF staining, and to quantify protein and mRNA levels of cell cycle regulators and SASP factors. These methods can be applied to the assessment of senescence in various models and tissues.

Cellular senescence, the irreversible state of cell-cycle arrest, can be induced by various cellular stresses. Here, we describe protocols to induce cellular senescence and methods to assess markers of senescence.

Techniken zur Induktion und Quantify Zelluläre Seneszenz

In response to cellular stress or damage, proliferating cells can induce a specific program that initiates a state of long-term cell-cycle arrest, termed ...

Volume Segmentation and Analysis of Biological Materials Using SuRVoS (Super-region Volume Segmentation) Workbench

Segmentation is the process of isolating specific regions or objects within an imaged volume, so that further study can be undertaken on these areas of interest. When considering the analysis of complex biological systems, the segmentation of three-dimensional image data is a time consuming and labor intensive step. With the increased availability of many imaging modalities and with automated data collection schemes, this poses an increased challenge for the modern experimental biologist to move from data to knowledge. This publication describes the use of SuRVoS Workbench, a program designed to address these issues by providing methods to semi-automatically segment complex biological volumetric data. Three datasets of differing magnification and imaging modalities are presented here, each highlighting different strategies of segmenting with SuRVoS. Phase contrast X-ray tomography (microCT) of the fruiting body of a plant is used to demonstrate segmentation using model training, cryo electron tomography (cryoET) of human platelets is used to demonstrate segmentation using super- and megavoxels, and cryo soft X-ray tomography (cryoSXT) of a mammalian cell line is used to demonstrate the label splitting tools. Strategies and parameters for each datatype are also presented. By blending a selection of semi-automatic processes into a single interactive tool, SuRVoS provides several benefits. Overall time to segment volumetric data is reduced by a factor of five when compared to manual segmentation, a mainstay in many image processing fields. This is a significant savings when full manual segmentation can take weeks of effort. Additionally, subjectivity is addressed through the use of computationally identified boundaries, and splitting complex collections of objects by their calculated properties rather than on a case-by-case basis.

Volume Segmentation and Analysis of Biological Materials Using SuRVoS Super-region Volume Segmentation Workbench

Segmentation of three-dimensional data from many imaging techniques is a major bottleneck in analysis of complex biological systems. Here, we describe the use of SuRVoS Workbench to semi-automatically segment volumetric data at various length-scales using example datasets from cryo-electron tomography, cryo soft X-ray tomography, and phase contrast X-ray tomography techniques.

Volumen-Segmentierung und Analyse von biologischen Materialien mit SuRVoS (Super-Region Volumen Segmentierung)-Workbench

Segmentation is the process of isolating specific regions or objects within an imaged volume, so that further study can be undertaken on these areas of ...