Open Microscopy Environment

Video in TIB AV-Portal: Open Microscopy Environment

Formal Metadata

Open Microscopy Environment
Informatics for Biological Imaging
Title of Series
CC Attribution 2.0 Belgium:
You are free to use, adapt and copy, distribute and transmit the work or content in adapted or unchanged form for any legal purpose as long as the work is attributed to the author in the manner specified by the author or licensor.
Release Date

Content Metadata

Subject Area
The Open Microscopy Environment (OME) is an open-source software framework for addressing informatics challenges in biological imaging and analysis: proprietary file formats, lack of storage, and analysis facilities and standards for sharing image data and results. The Java-based OMERO client-server platform and its model-based architecture is applicable to a range of imaging domains, including light and electron microscopy, high-content screening, and recently into applications using non-image data from clinical and genomic studies. Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges [1]. OME has three components—an open data model for biological imaging; standardised file formats (OME-TIFF) and software libraries for file conversion (Bio-Formats [2]); and a software platform for image data management and analysis (OMERO [3]). In this presentation, we discuss the design and use of OMERO. The Java-based OMERO client-server platform [3] comprises an image metadata store, an image data repository, visualization and analysis by remote access, enabling sharing and publishing of image data. OMERO.grid [4] facilitates distributed computing including scripting facility for image processing. OMERO.grid manages processes across nodes, providing distributed background processing, log handling, and several other features, using ZeroC's IceGrid framework [5]. Several third-party applications use the OMERO API (e.g. image-based searching, tracking and automatic image tagging; sophisticated image analysis modules [6]). OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high-content screening, and recently into applications using non-image data from clinical and genomic studies [7]. Our next version, OMERO-5 improves support for large datasets, and reads images directly from their original file format, allowing access by third-party software. OMERO and Bio-Formats run the JCB DataViewer [8] online scientific image publishing system and other institutional image data repositories [9], [10].
Computer animation 1 (number) Planning Right angle Mereology Theory
Particle system Computer animation Thermodynamisches System Multiplication sign Right angle Funktionalanalysis Mereology
Computer program Group action Image resolution Physical law Shared memory 1 (number) Instance (computer science) Cartesian coordinate system Word Computer animation Vector space Thermodynamisches System Data storage device Business model Quicksort
User interface Complex analysis Computer animation Open source Execution unit Form (programming)
Point (geometry) Service (economics) Open source Execution unit Mathematical analysis Set (mathematics) Mereology Product (business) Data model Computer animation Visualization (computer graphics) Order (biology) Summierbarkeit Resultant Library (computing)
Web page Point (geometry) Information Software developer Multiplication sign Projective plane Electronic mailing list Basis <Mathematik> Variable (mathematics) Machine vision Computer animation Website Quicksort Task (computing)
Point (geometry) Service (economics) Computer animation Data structure Extension (kinesiology) Theory Formal language
Algorithm Linear regression Multiplication sign Displacement Mapping Projective plane Basis <Mathematik> Mereology Event horizon Dimensional analysis Type theory Digital photography Computer animation Software Different (Kate Ryan album) Personal digital assistant Operator (mathematics) Video game Pattern language Position operator Writing Form (programming) Social class
Process (computing) Computer animation Open source Observational study Software developer Multiplication sign Projective plane Business model Bilderkennung Task (computing) Power (physics)
Computer animation Bit rate Software Term (mathematics) Internetworking Projective plane Pressure
Computer animation Query language Term (mathematics) Direction (geometry) Electronic mailing list Self-organization Right angle Bit Musical ensemble
Web page Computer program Pulse (signal processing) Context awareness Group action Service (economics) Vapor barrier Computer file Multiplication sign Spiral Set (mathematics) Water vapor Mereology Rule of inference Metadata Derivation (linguistics) Meeting/Interview Database Authorization Energy level Data structure Area Graph (mathematics) Chemical equation Projective plane Physical law Shared memory Subgraph Line (geometry) Entire function Category of being Word Software Personal digital assistant Universe (mathematics) Right angle Summierbarkeit Pressure Library (computing)
check in the room but this is because they the ones from the original right and the left and the right thing to do at and in the theory that you can think of the of the a lot of this end of the origin of the use of the fact that you are part of the plan the was you
have lost all kind of all over the world by external than the from it could also be that from this hot that
who is the world of the posts along this the and what is not their 1st month of the year by the end of the end of this kind of data and according to the united in and the war and this is going to look at the the at the time of the lectures that were part of the of the of the of by the by the size of the end and images and things like that the White House on the the function of the of the of the of time if you and this year those of the particle so they could just as the universe of of the basal remained some of the the people around the world and this and this and some of the people the and and to find the of this of so axis of the rights of the lack of a review of the the the the the the the the 1st half of the people in the world and of the system that we have the money and uh names of all of the the
the the real 1 of the things I want to elaborate on the data instances of the and it's they kind of you know that that was the 1st to next that both the more formal the vector of the law in the the environment and the best of my knowledge sharing and they found that if you have a very very hard frustrated that you want to the work of this kind of people at the at the end of it because of the the uh the resolution of the body and also on the axis of all of the of the and what about the so in the normal 1 might have some knowledge of
the data so that sort of thing on the face of this program is to this it is the users and the preservation and storage of we don't solve all problems for a the scientist and try to solve the ones that are the most we also have a group of people which have published after the words of the model in the that's all we try to do this because they looks at the
end of this unit is an example of the of the the the the the speed of light the thing and that allows users to interact with the he's going to the data and the the number of that that that you are in the heart of the matter was used in the running of the source of the that's the problem with that is something that there are any of these forms of the world and and so you can use more of what kind just I
also mentioned that the communities to come I also mentioned to you and your example you think this is the goal of the of the of the of of the of the of the book value of the day that complexity also means that the user interfaces of the kind of thing you you kind of sound and or the use of this so that they are 2 and
we have never been done in this is the topic of our data model around the so that all the from it was using example uh this indicates that the data used in this the setting of a lot source of data and all the all the requirements of X is the sum of the parts used in the middle of it will be due the landing on the analysis of all the other 2 parts of the body which of these units and the sum of of the of the and going on they may be the size of the of the and that's fine as long as I know where the product of the or any of the work of some of the people of the the of the of the but I think the world
uh looking at this from this point and and there is a service to the basic things on the order of on the and on the same I want the the end of the year of the points the and there are 2 kinds of the visualization of the and the work of the start of this place and this is the 1st people in the library in order to search and you might think that this kind of of the the 2 the rest of the results the and find of the this is
a list of the of the of the of the inaccessibility of the page and the vision of the letters of the of the of the of the the the the the of the other people's songs and I mentioned before the idea of the people in the world you just interest around the world of the size of at the beginning of the the year the example of the images in a lot of variability the 2
right thank you very similar to the end of the war was also running at the end of the data from the amount of data and projects of the information in the image of a like this 1 in the world and this site this uses this was that the the camps this is the from time to time by like the way of my favorite topics this is to uh prompted users around here and we also extensible so in the generated from sort by science of art on this the basis of the point but also the the available annotated of people in the development of the task of the use of its uh rendering and the users of the of the of the afterward we don't want have a chance to get a really all that remains at the same time people and then on the end of the story of the of so accessibility and out the so related the so you
bring it is a place where you can be certain that you lose the of of those qualities that you and and just the expense of the the extent service on the service and we have restricted and you can run the thing on the ground structure and lot of what we get from from the sea so we the theory
of it is also a point right the language of the of the of the of the of so what is it
about the world really right all the interesting because it's a hundreds of thousands of dimensions so that was the rest of the world and it also so what generally happens there is some specific position of the center of the system so that it has this form the oral and television or something like what you would want to go just like also we have a we have about 12 different types of patterns in a different form of the class and each of those after really analyzed in the in the in the event of a small of the the XML we starting from the generic tools which can then be used by a lot of the so it is
from the so so I think is so as a natural part of the software to become so the goal of this what was just too afraid of that kind of treatment of the place and and all that is part of the writing of I the regression algorithms that have a lot of software that is the case for the 1st of your life so the best of that so so that is the goal of the book you know we redesigned the bias of the Leverage existing so I'm going to the original happens with right media with all operation of the that people want to I will be working out is the what are the photographs the basis of the project so as to I got to where we were following way and the a lot of agencies and realizing more it's more expensive and I would love to have project of sufficient quality of the Antarctica from time and this would be realized that the money and they said the was same thing as that just the possible to have the capital of the world of as you can see in the knowledge of the and the character displacement so all this is what the your take on that but also by the producer and reliance on the other side they will be able to use computers and for the life of the of of the the the world the
so that was the source of all of the of the data and the this is just this just in the of investment projects funding by those who is the best quality use of we try to actively solicit developers who working in in of the model to what the oxygen is that most of the time the individuals which they actually uses the about the have been just as I the comes on tools and
image analysis and power and wealth of various tasks which it is 1 of most and this the model is quite a lot of work with some useful at the hands of the people of course which of the of the now if if projects and the originality of this book will to get the the the study of the rest of the job of what
actually happened dictated by the original have so the Americans the
European project of the motion of the of the dual licensed software really crucial this and as a way of working without having to facilitate the Commission has lots of things happen to release some of them as well a lot bigger to be so low that is beginning to use the internet as a primary and appositional and mostly just the rate of heart disease pressure from from users of the rest of the all right so a lot of friends and also provides physical disposal you don't just 1 also in terms of which engagement of the
so we're funded by the Wellcome Trust so we are solving historical reasons but generally I wanted direction in terms of music so we're trying to build a list people so so the right there if you I have a bit more about me is itself so that the organization of the and the original query the has this feature of it so
this the end of the listed the 1st to put without it was so that was the last
year gain said that writing all the problem but I know that the work at the and so area of of the you would use the same set of the that and so you you have what what what was going on in the world was that the rest of the things that has the same research subgraphs in the area of the universities and research this will be often the stationary and creating software from the pages the 1 you want that's the answer sovereignty is from general or a of the of labels are cancer will be on your way to the area of the projects that would focus this is all right so about it's always I think it's is fundamentally organized so the project useful was always the pressure which is well and the growth of what the expense of others that but I think that this is not the sole knowledge this the 2nd and the level of the so here some of the and the other parts of the world to something like that and I think this is the way so that if you let them know the matter of the published on the use of of the of the and here is what is the opposite of what 1 might arise so they have the same you they have be in the in the in the world of work for the time of the graph for so it's always have to provide a a lot of things wrong with published specific and in in the 1st for all the different forms of or do I have to to go on and on and on and on and on to provide a service so far they still act sums this a certain level of cooperation with the words that this happens viable such library which used to be and so how much they collaborate and how easy it was like a whole lot of the lowers the barrier in harmony with this and when they are not going to get find the balance of wasn't used to send us to study this year some of the rest of the rules of the work in this line of culture lines in the design of any 2 of them with some of the data in the work of a of a and it's also means the spiral as used in the community think many of you like like this they should be aligned of the of the world it is affecting the use of the about the use in this part of the of of environment and of the thing that I think we covered this for 127 in this new those here to the and to work work this I don't know what you think of as far as I know that you already know what we know about the actual level of this you know the the normal so I think that is a derivation of the are intentionally trying to to the exactly that the I think that the origin program sharing of the they want to know why the share of the thinking about this time of I'm oxidation and a a lot of most of this the price of the so as once the around the entire set of course you know what the people that provides always of this follows file directly and you go over the years of the government structure and you the would it really depends on behalf of the of the resources to do that I think sometimes it's itself on on the right and the idea is very high of the have a knowledge of the pulses of metadata in database of all the I would be the case here is that the kind of part the of times of the the stuff going on but I think that the features of this I think is lot of that makes the reason the name of the author of the world has and the possibility of of the audience and all of that was 1 of the problems with this so you are going to from the ideas of the thing I you don't have to be built in law in the original In the I've finally found that there was a lot of that so that more the reason the group of people who believe in the context of the the the the the the the the the point of in is thing at the end of the water that provides the size of the of the of the of the the of the of the of the of the of the of the special properties of this yeah the woman with a