DMBI: Data Management for Bio-Imaging.

Transcription

1 DMBI: Data Management for Bio-Imaging. Questionnaire Data Report

2 1.0 Overview As part of the DMBI project an international meeting was organized around the project to bring together the bio-imaging community around the theme of data management. This meeting, OMERO.inAction, was held on the 6 th of April 2011 and involved over 70 delegates. As part of the event registration delegates were asked to fill in a questionnaire to capture the delegate s views about data management. This mini report contains the findings from the questionnaires of 45 delegates.

3 Question 1.0: What type of microscopes are used at your institute? Other: 2 Photon, PALM / STORM and OPERA. Question 2.0: At what level are you interested in data managment?

4 Question 3.0: How much data is produced per year at this level? Question 4.0: What kind of image file sizes do you work with?

5 Question 5.0: How do you currently manage your data? Other: Home made solution. Question 6.0: How do you process your imaging data? Other: Acapella (3), Amira, Cell Profiler (3), CLSM software, EMAN/Chimera, Home made, Huygens (2), ImageMagick, In-house lifetime, Photoshop, Python, SoftWorx, Tigris, Volocity (8).

6 Question 6.0: Rank the following features in order of importance to you? * (higher is more important) Question 7.0: What are the main challenges in the data management of biological images? First of all, that users do any management at all. Comprehensive storage of large amount of images. Automatisation of common postprocessing tasks deconvolution, channel alignment,... Metadata and output management Being able to organize the huge amount of 2D,3D and 4D images generated in my/our group experiments in a coherent way. have an easy link from images to description of experiment done. being able to keep track of the changes done to images having a track that takes you easily back to the original images. being able to work with images gathered with different microscopes which are stored in different types of files. have an easy conversion of types of files. being able to easily share image data with other members of the group. all of this minimizing the amount of data produced. Easy data finding and sharing Preservation and addition of image metadata - organization of image datasets for efficient retrieval - dealing with a variety of image data formats - ease of access to image data for viewing and analysis - efficient data storage and backup

7 There s too much of it, and once the researcher leaves it s effectively gone forever. To manage the vast amounts of biological images generated using high throughput microscopy; to easily access and interpret biological images; to capture, record and represent efficiently the metadata associated to every image; to work with and share large size images As a user of microscope bright field, confocal and high-throughput software and equipment, there are several points which are important to my mind. First of all, the amount of data created is more and more important each year, notably with the High-Throughput microscope OPERA, which require organizing the data in order to be able to find recent or older images with the experimental conditions and data generated from the analysis. The OMERO software could simplify this operation by storing the images with the metadata and to display them with a user-friendly interface. So to simplify and/or automate data management and analysis in between the different users of a specific equipment is becoming a critical challenge. The second main challenge is data sharing. In fact, it is sometimes difficult to share images for several reasons like the size of the data to transfer, the extension type of the file which require having the appropriate software... This platform would allow us to securely transfer data and the related metadata in an OME file format. The third point is, data export. In fact, the finality of a research program is to share the work in congress and to publish articles. And nowadays, the data quality required is more and more high. The other point is that before sharing data, you have to interpret them, and for that, a nice presentation is really helpful. So the ability of quickly export figures, tables... is really important in order to produce high quality presentation as well as helping the researcher to interpret the data. Modern microscopy techniques produce large amounts of image data. This needs to be effectively managed to avoid losing critical experiment data. In addition the large volume of data cannot be processed manually and thus highly automated analysis platforms are required. As time progresses new techniques will be developed that can be retroactively applied to past data. This will require a large scale processing platform capable of automation. Digital archiving and preservation will become increasingly important as image formats change. It is essential that old images be maintained in a state that can be accessed by modern software. Large amount of large data files, hard to store, at the same time the access for multiple users must be provided, as data analysis is needed Synchronization between various applications Images are usually associated with an individual and are lost when these people leave or if they do not back up data properly. Images are also not searchable. Need to integrate; multiple capture formats, iterative processing and extra info for long-term storage

8 of images to work. Time course experiments can generate huge data sets. Requirement to keep for x years, find them after x years. gain meaningful results from them Metadata capture, difficulties with file formats, ever increasing data sizes with automated instruments Automation, storage, and the construction/maintenance of analysis pipelines. Too many image formats that can t all be processed with any single analysis program. User friendliness, affordability, reliability, flexibility Central facility archiving, backup and access versus individual user storage. Persuading the microscope users to us a standard system. Keeping track of all meta data for an experimental set of images Associated annotations/meta data with images. Combine multi scale data to useful views Definition and curation of metadata Analysing and quantifying differences between images, and storage. Quantification of depicted biological structures Storage and retrieval of images Create scripts to manipulate image data Being able to quantify data in a competitive time frame. This requires the development of user friendly tools that can cope with complex images.

9 Data storage, archiving strategies, datasets and link to other experimental documentation Storage, visualization and analysis of generated images. Question 8.0: Based on your present knowledge what are the most attractive features of OMERO? Impressive client GUI. Image analysis potential on large sets of images. Potential for a "biologistfriendly" and therefore used images database. Open source easy track of images and changes done on images. easy share of images. Data management tool developed by and for the bio-imaging community, for annotation and sharing of image data - convenient client/server model for secure, scalable, central data storage combined with ease of access for viewing and analysis - open source; possibilities for image analysis development The fact that it s already built, and my tiny little crew doesn t have to build it. Scripting Service, Image processing, Measure, Figure Export, Metadata, 3D Projection, Add Experiment Info The main attractive features of OMERO are first, the capacity of the software to read different file format created by all the different equipment in the laboratory. This would be a great interface between the instrument software and the data analysis software. In fact this is linked to the second attractive feature, as actually we are running different image analysis software in order to "transform" images into interpretable data. This would allow us to analyse images taken from many different equipment by the most accurate software or to perform the image processing directly via OMERO to have comparable data and to export directly paper quality tables or figures. Last but not least, the ability of the software to securely share data between users via a web interface makes OMERO a powerful tool to interpret results and to create new interactions between laboratories. As metadata scale, equipment used,... are also integrated to the images, the different users can also be sure of what they are looking at, and give them the possibility to reproduce an experiment to confirm or infirm the results in an independent way.

10 OMERO offers a scalable, centralised platform for managing our image data. It will allow users to upload images for archiving and perform data analysis using client software that can be run on any machine. The open source nature of OMERO allows our users to install the clients on any machine thus avoiding the prohibitive costs of other software products. OMERO allows access to images to multiple clients without the need to store them, allows data analysis on them free Organisation of the images and data as well as being able to search for particular images. It is important though to have credit where credit is due. Searchability of images ability to include extra info, degree of image manipulation possible. database, ability to analyse, platform independence The fact that it has a thriving community, supports a wide range of formats and is developed in the open. I hope to learn more. Can handle most image formats and can store data securely on a server open source, low cost so far, sufficient functionality User interface and open access Wide range of file formats True relational database for appending experimental plans and results directly to the raw data, as well as a pretty good search facility

11 Centralised database with which image analysis software can interact. Annotations, Extensibility Archive, and basic image processing I don t know anything about omero Image management/organization Provides a image database management system Open Source with a strong community and a supportive development team The clients provide easily accessable imaging tools Web access and group working Server side data manipulation linking image processing with central storage. centralised data/image management solution Question 8.0: What do you hope to gain from the OMERO.inAction meeting? We just acquired a API-OMX high resolution microscope and we think it s the moment to install in our facility a serious storage system like OMERO. I would like to meet the developers, gather information on its possibilities (server based image treatment and analysis), train my self in its usage and administration. Understanding how to implement OMERO for my own experiments and in my current group as well as understanding how to implement it in the future in other groups. We currently have an OMERO server installed in the department, which I plan to start using. I would also like to incorporate some of the image analysis routines I have written into our OMERO server, and I have installed a personal test OMERO server for this purpose. However, I would definitely benefit from

12 some tuition and discussion of OMERO with experts. Finally, I have been shortlisted for a job interview in the department for an Image Analysis Specialist position - should I be successful with my application, I would be involved in helping other microscope users in the department with curation and analysis of their data. A sense of how to approach building an institute-wide system for managing the firehose of data coming from our microscopes. To become familiar with the OMERO concept and to learn to efficiently manage and process my biological data First of all, I think that OMERO is clearly from interest for our Lab. What I hope to gain from this meeting is first of all to interact with future users and users of OMERO to have an overview of the needs and what is actually available in term of data sharing, methodology and image analysis. In fact, I would like to know how OMERO is actually used in the different labs and how people intend to use this platform. Secondly, I would gain by "using" the OMERO platform software in order to have an idea of the accessibility of the software as well as to raise ideas of how to use it in our lab. Finally, a practical approach to the software could really help me understand the features of the software, to transfer this knowledge to potential users within my team and the laboratory. We have been trialling OMERO at our institution for the storage of image data. I have recently joined the group with the responsibility for developing image analysis routines. I hope to gain knowledge of the overall architecture of OMERO and how to develop software to run on the OMERO server to analyse images. To understand how this exactly works and what is needed for it in detail. As we are going to use this system for our 2P microscope images analysis, it is quite crucial deeper insight, practical tips A greater understanding of the capabilities, recent updates and to see how it has been implemented at other institutes. Contributor. But also to learn more about OMERO as an RDM solution. Greater understanding of OMERO, how does it work in other institutions. OMERO in the future

13 a better feel for implementation and use. We plan to use OMERO here in Manchester and I m hoping to benefit from others experience in setting it up and using it. Understand the options available at JIC Learn about useful features of OMERO that will help me analyse my data quickly and effectively learn what it can do for me in helping me quantify staining on some immunohistochemistry. Overview, assessment of feasibility, exchange with experienced users, discussion Learn more about OMERO An idea as to how OMERO could integrate with our FLIM data requirements. More info about adding experimental data and using the scripting for analysis How OMERO deals with image metadata See how we can progress with the deployment of OMERO at the London Research Institute Cancer Research UK Feedback on possible applications for EBI To learn about omero Ideas about efficient management and processing of experimental images Find out how others who have implemented OMERO manage the data Move forward into scripting and image data manipulation Network

14 New ideas about how to analyse complex 5D data sets obtained from time-lapse microscopy. General idea on how to setup omero in a multi-centered enviroment features of OMERO solution A good understanding of OMERO and how it can be used within our institute.