Review of free software tools for image analysis of fluorescence cell micrographs
Summary An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guid...
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| Veröffentlicht in: | Journal of microscopy (Oxford) 2015-01, Vol.257 (1), p.39-53 |
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| creator | WIESMANN, V. FRANZ, D. HELD, C. MÜNZENMAYER, C. PALMISANO, R. WITTENBERG, T. |
| description | Summary
An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guidelines about which tools the users should use to segment fluorescence micrographs. We selected 15 free tools and divided them into stand‐alone, Matlab‐based, ImageJ‐based, free demo versions of commercial tools and data sharing tools. The review consists of two parts: First, we developed a criteria catalogue and rated the tools regarding structural requirements, functionality (flexibility, segmentation and image processing filters) and usability (documentation, data management, usability and visualization). Second, we performed an image processing case study with four representative fluorescence micrograph segmentation tasks with figure‐ground and cell separation. The tools display a wide range of functionality and usability. In the image processing case study, we were able to perform figure‐ground separation in all micrographs using mainly thresholding. Cell separation was not possible with most of the tools, because cell separation methods are provided only by a subset of the tools and are difficult to parametrize and to use. Most important is that the usability matches the functionality of a tool. To be usable, specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well‐structured menu and intuitive graphical user interface.
Lay Description
Fluorescent micrographs depicting cell and cell structures are essential for many experiments in medicine and life sciences. For the assessment of such micrographs automatic and semi‐automatic image analysis tools, and more specifically, segmentation methods are essential. There are many free software tools available to assist scientists to assess fluorescence micrographs in various studies. Nevertheless, not every tool is suited for all users with little or no knowledge in image processing.
Within this work we reviewed 15 free image processing tools for fluorescence micrographs evaluations and compared them in a twofold study: First, we developed a criteria catalogue and rated the tools regarding their usability, functionality and installation. Second, we performed an image processing case study and tried to solve typical image processing problems in fluorescen |
| doi_str_mv | 10.1111/jmi.12184 |
| format | Article |
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An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guidelines about which tools the users should use to segment fluorescence micrographs. We selected 15 free tools and divided them into stand‐alone, Matlab‐based, ImageJ‐based, free demo versions of commercial tools and data sharing tools. The review consists of two parts: First, we developed a criteria catalogue and rated the tools regarding structural requirements, functionality (flexibility, segmentation and image processing filters) and usability (documentation, data management, usability and visualization). Second, we performed an image processing case study with four representative fluorescence micrograph segmentation tasks with figure‐ground and cell separation. The tools display a wide range of functionality and usability. In the image processing case study, we were able to perform figure‐ground separation in all micrographs using mainly thresholding. Cell separation was not possible with most of the tools, because cell separation methods are provided only by a subset of the tools and are difficult to parametrize and to use. Most important is that the usability matches the functionality of a tool. To be usable, specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well‐structured menu and intuitive graphical user interface.
Lay Description
Fluorescent micrographs depicting cell and cell structures are essential for many experiments in medicine and life sciences. For the assessment of such micrographs automatic and semi‐automatic image analysis tools, and more specifically, segmentation methods are essential. There are many free software tools available to assist scientists to assess fluorescence micrographs in various studies. Nevertheless, not every tool is suited for all users with little or no knowledge in image processing.
Within this work we reviewed 15 free image processing tools for fluorescence micrographs evaluations and compared them in a twofold study: First, we developed a criteria catalogue and rated the tools regarding their usability, functionality and installation. Second, we performed an image processing case study and tried to solve typical image processing problems in fluorescence micrograph evaluation with the evaluated tools. The evaluation consisted of the detection of cells, the discrimination between cells and image background, and the separation of touching or overlapping cells.
The tools reviewed under the criteria catalogue showed that they display a wide range of functionality and usability. In the image processing case study, we were able to perform fore‐and background separation in all micrographs. Cell separation was not possible with most of the tools as such methods are provided only by a subset of the tools and are difficult to parameterize and to use.
Our main findings are that only tools with both, high usability as well as high functionality, are most likely applicable to many use‐cases. Specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well‐structured menu and intuitive GUI. Finally, we give recommendations and suggestions for potential users for when to use which tool for an automated assessment of fluorescence micrographs.</description><identifier>ISSN: 0022-2720</identifier><identifier>EISSN: 1365-2818</identifier><identifier>DOI: 10.1111/jmi.12184</identifier><identifier>PMID: 25359577</identifier><identifier>CODEN: JMICAR</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Cell segmentation ; fluorescence microscopy ; image analysis ; Image processing systems ; Image Processing, Computer-Assisted - methods ; Microscopy, Fluorescence ; Software ; usability</subject><ispartof>Journal of microscopy (Oxford), 2015-01, Vol.257 (1), p.39-53</ispartof><rights>2014 Fraunhofer‐Institute for Integrated Circuits IIS Journal of Microscopy © 2014 Royal Microscopical Society</rights><rights>2014 Fraunhofer-Institute for Integrated Circuits IIS Journal of Microscopy © 2014 Royal Microscopical Society.</rights><rights>Journal compilation © 2015 Royal Microscopical Society</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4194-25b9ff2dd07798c131853e726707b77cdb7292bf9aae7367f56b1b616739cdb23</citedby><cites>FETCH-LOGICAL-c4194-25b9ff2dd07798c131853e726707b77cdb7292bf9aae7367f56b1b616739cdb23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fjmi.12184$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fjmi.12184$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,1427,27903,27904,45553,45554,46388,46812</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25359577$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>WIESMANN, V.</creatorcontrib><creatorcontrib>FRANZ, D.</creatorcontrib><creatorcontrib>HELD, C.</creatorcontrib><creatorcontrib>MÜNZENMAYER, C.</creatorcontrib><creatorcontrib>PALMISANO, R.</creatorcontrib><creatorcontrib>WITTENBERG, T.</creatorcontrib><title>Review of free software tools for image analysis of fluorescence cell micrographs</title><title>Journal of microscopy (Oxford)</title><addtitle>J Microsc</addtitle><description>Summary
An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guidelines about which tools the users should use to segment fluorescence micrographs. We selected 15 free tools and divided them into stand‐alone, Matlab‐based, ImageJ‐based, free demo versions of commercial tools and data sharing tools. The review consists of two parts: First, we developed a criteria catalogue and rated the tools regarding structural requirements, functionality (flexibility, segmentation and image processing filters) and usability (documentation, data management, usability and visualization). Second, we performed an image processing case study with four representative fluorescence micrograph segmentation tasks with figure‐ground and cell separation. The tools display a wide range of functionality and usability. In the image processing case study, we were able to perform figure‐ground separation in all micrographs using mainly thresholding. Cell separation was not possible with most of the tools, because cell separation methods are provided only by a subset of the tools and are difficult to parametrize and to use. Most important is that the usability matches the functionality of a tool. To be usable, specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well‐structured menu and intuitive graphical user interface.
Lay Description
Fluorescent micrographs depicting cell and cell structures are essential for many experiments in medicine and life sciences. For the assessment of such micrographs automatic and semi‐automatic image analysis tools, and more specifically, segmentation methods are essential. There are many free software tools available to assist scientists to assess fluorescence micrographs in various studies. Nevertheless, not every tool is suited for all users with little or no knowledge in image processing.
Within this work we reviewed 15 free image processing tools for fluorescence micrographs evaluations and compared them in a twofold study: First, we developed a criteria catalogue and rated the tools regarding their usability, functionality and installation. Second, we performed an image processing case study and tried to solve typical image processing problems in fluorescence micrograph evaluation with the evaluated tools. The evaluation consisted of the detection of cells, the discrimination between cells and image background, and the separation of touching or overlapping cells.
The tools reviewed under the criteria catalogue showed that they display a wide range of functionality and usability. In the image processing case study, we were able to perform fore‐and background separation in all micrographs. Cell separation was not possible with most of the tools as such methods are provided only by a subset of the tools and are difficult to parameterize and to use.
Our main findings are that only tools with both, high usability as well as high functionality, are most likely applicable to many use‐cases. Specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well‐structured menu and intuitive GUI. Finally, we give recommendations and suggestions for potential users for when to use which tool for an automated assessment of fluorescence micrographs.</description><subject>Cell segmentation</subject><subject>fluorescence microscopy</subject><subject>image analysis</subject><subject>Image processing systems</subject><subject>Image Processing, Computer-Assisted - methods</subject><subject>Microscopy, Fluorescence</subject><subject>Software</subject><subject>usability</subject><issn>0022-2720</issn><issn>1365-2818</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp10E1PwyAcBnBiNG5OD34BQ-JFD92AFihHs_gyM2M0em5o-2d2aceE1WXfXrZODyZy4cAvT3gehM4pGdJwRvOmGlJG0-QA9WkseMRSmh6iPiGMRUwy0kMn3s8JISlPyTHqMR5zxaXso5dX-Kpgja3BxgFgb81qrR3glbW1x8Y6XDV6BlgvdL3xld_JurUOfAGLAnABdY2bqnB25vTyw5-iI6NrD2f7e4De727fxg_R9Pl-Mr6ZRkVCVRIxnitjWFkSKVVa0JimPAbJhCQyl7Ioc8kUy43SGmQspOEip7mgQsYqPLJ4gK663KWzny34VdZUfvsZvQDb-owKppTkPBGBXv6hc9u6UGinUpXEKlFBXXcqVPHegcmWLnR3m4ySbLtzFnbOdjsHe7FPbPMGyl_5M2wAow6sqxo2_ydlj0-TLvIbNvmGDQ</recordid><startdate>201501</startdate><enddate>201501</enddate><creator>WIESMANN, V.</creator><creator>FRANZ, D.</creator><creator>HELD, C.</creator><creator>MÜNZENMAYER, C.</creator><creator>PALMISANO, R.</creator><creator>WITTENBERG, T.</creator><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7U5</scope><scope>8FD</scope><scope>L7M</scope><scope>7X8</scope></search><sort><creationdate>201501</creationdate><title>Review of free software tools for image analysis of fluorescence cell micrographs</title><author>WIESMANN, V. ; FRANZ, D. ; HELD, C. ; MÜNZENMAYER, C. ; PALMISANO, R. ; WITTENBERG, T.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4194-25b9ff2dd07798c131853e726707b77cdb7292bf9aae7367f56b1b616739cdb23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Cell segmentation</topic><topic>fluorescence microscopy</topic><topic>image analysis</topic><topic>Image processing systems</topic><topic>Image Processing, Computer-Assisted - methods</topic><topic>Microscopy, Fluorescence</topic><topic>Software</topic><topic>usability</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>WIESMANN, V.</creatorcontrib><creatorcontrib>FRANZ, D.</creatorcontrib><creatorcontrib>HELD, C.</creatorcontrib><creatorcontrib>MÜNZENMAYER, C.</creatorcontrib><creatorcontrib>PALMISANO, R.</creatorcontrib><creatorcontrib>WITTENBERG, T.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Technology Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of microscopy (Oxford)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>WIESMANN, V.</au><au>FRANZ, D.</au><au>HELD, C.</au><au>MÜNZENMAYER, C.</au><au>PALMISANO, R.</au><au>WITTENBERG, T.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Review of free software tools for image analysis of fluorescence cell micrographs</atitle><jtitle>Journal of microscopy (Oxford)</jtitle><addtitle>J Microsc</addtitle><date>2015-01</date><risdate>2015</risdate><volume>257</volume><issue>1</issue><spage>39</spage><epage>53</epage><pages>39-53</pages><issn>0022-2720</issn><eissn>1365-2818</eissn><coden>JMICAR</coden><abstract>Summary
An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guidelines about which tools the users should use to segment fluorescence micrographs. We selected 15 free tools and divided them into stand‐alone, Matlab‐based, ImageJ‐based, free demo versions of commercial tools and data sharing tools. The review consists of two parts: First, we developed a criteria catalogue and rated the tools regarding structural requirements, functionality (flexibility, segmentation and image processing filters) and usability (documentation, data management, usability and visualization). Second, we performed an image processing case study with four representative fluorescence micrograph segmentation tasks with figure‐ground and cell separation. The tools display a wide range of functionality and usability. In the image processing case study, we were able to perform figure‐ground separation in all micrographs using mainly thresholding. Cell separation was not possible with most of the tools, because cell separation methods are provided only by a subset of the tools and are difficult to parametrize and to use. Most important is that the usability matches the functionality of a tool. To be usable, specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well‐structured menu and intuitive graphical user interface.
Lay Description
Fluorescent micrographs depicting cell and cell structures are essential for many experiments in medicine and life sciences. For the assessment of such micrographs automatic and semi‐automatic image analysis tools, and more specifically, segmentation methods are essential. There are many free software tools available to assist scientists to assess fluorescence micrographs in various studies. Nevertheless, not every tool is suited for all users with little or no knowledge in image processing.
Within this work we reviewed 15 free image processing tools for fluorescence micrographs evaluations and compared them in a twofold study: First, we developed a criteria catalogue and rated the tools regarding their usability, functionality and installation. Second, we performed an image processing case study and tried to solve typical image processing problems in fluorescence micrograph evaluation with the evaluated tools. The evaluation consisted of the detection of cells, the discrimination between cells and image background, and the separation of touching or overlapping cells.
The tools reviewed under the criteria catalogue showed that they display a wide range of functionality and usability. In the image processing case study, we were able to perform fore‐and background separation in all micrographs. Cell separation was not possible with most of the tools as such methods are provided only by a subset of the tools and are difficult to parameterize and to use.
Our main findings are that only tools with both, high usability as well as high functionality, are most likely applicable to many use‐cases. Specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well‐structured menu and intuitive GUI. Finally, we give recommendations and suggestions for potential users for when to use which tool for an automated assessment of fluorescence micrographs.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>25359577</pmid><doi>10.1111/jmi.12184</doi><tpages>15</tpages></addata></record> |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete; Wiley Online Library Free Content |
| subjects | Cell segmentation fluorescence microscopy image analysis Image processing systems Image Processing, Computer-Assisted - methods Microscopy, Fluorescence Software usability |
| title | Review of free software tools for image analysis of fluorescence cell micrographs |
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