Talk:Embryo Virtual Slides

From Embryology


Virtual Slides on the Web


A virtual microscope for academic medical education: the pate project

Brochhausen C1, Winther HB, Hundt C, Schmitt VH, Schömer E, Kirkpatrick CJ.


BACKGROUND: Whole-slide imaging (WSI) has become more prominent and continues to gain in importance in student teaching. Applications with different scope have been developed. Many of these applications have either technical or design shortcomings. OBJECTIVE: To design a survey to determine student expectations of WSI applications for teaching histological and pathological diagnosis. To develop a new WSI application based on the findings of the survey. METHODS: A total of 216 students were questioned about their experiences and expectations of WSI applications, as well as favorable and undesired features. The survey included 14 multiple choice and two essay questions. Based on the survey, we developed a new WSI application called Pate utilizing open source technologies. RESULTS: The survey sample included 216 students-62.0% (134) women and 36.1% (78) men. Out of 216 students, 4 (1.9%) did not disclose their gender. The best-known preexisting WSI applications included Mainzer Histo Maps (199/216, 92.1%), Histoweb Tübingen (16/216, 7.4%), and Histonet Ulm (8/216, 3.7%). Desired features for the students were latitude in the slides (190/216, 88.0%), histological (191/216, 88.4%) and pathological (186/216, 86.1%) annotations, points of interest (181/216, 83.8%), background information (146/216, 67.6%), and auxiliary informational texts (113/216, 52.3%). By contrast, a discussion forum was far less important (9/216, 4.2%) for the students. CONCLUSIONS: The survey revealed that the students appreciate a rich feature set, including WSI functionality, points of interest, auxiliary informational texts, and annotations. The development of Pate was significantly influenced by the findings of the survey. Although Pate currently has some issues with the Zoomify file format, it could be shown that Web technologies are capable of providing a high-performance WSI experience, as well as a rich feature set. KEYWORDS: Internet; WSI; databases; e-learning; microscopy; telepathology; virtual microscopy; whole-slide imaging

PMID 25963527


  • Change lower case stage to Stage for clearer template naming structure. Some files on archive may have original naming.
  • Added templates to Carnegie Stages pages.




(this belongs in the Widget namespace, that does not yet exist on the Wiki)

Sample Frame

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PHP versions for URL filtering.

I managed to fix it by removing the "validate:url" parameter in the Widget:Iframe code.

src="" changed to src=""

It is an internal wiki, which means the security is not an issue.

Stage 13

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see also templates

Using image mapping towards biomedical and biological data sharing

Gigascience. 2013 Sep 23;2(1):12. doi: 10.1186/2047-217X-2-12.

Mohd Zaizi NJ1, Awang Iskandar DN. Author information


Image-based data integration in eHealth and life sciences is typically concerned with the method used for anatomical space mapping, needed to retrieve, compare and analyse large volumes of biomedical data. In mapping one image onto another image, a mechanism is used to match and find the corresponding spatial regions which have the same meaning between the source and the matching image. Image-based data integration is useful for integrating data of various information structures. Here we discuss a broad range of issues related to data integration of various information structures, review exemplary work on image representation and mapping, and discuss the challenges that these techniques may bring.

PMID 24059352

Open Microscopy Environment


Open Microscopy Environment

OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community.

  • OMERO is client-server software for visualization, management and analysis of biological microscope images.
  • Bio-Formats is a Java library for reading and writing biological image files. It can be used as an ImageJ plugin, Matlab toolbox, or in your own software.