storage_management
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storage_management [2021/08/31 14:21] yves |
storage_management [2022/09/15 19:48] (current) yves |
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| ===== Storage management ===== | ===== Storage management ===== | ||
| - | Storage is important in digital pathology. Image data can be subject to any of the [[https://en.wikipedia.org/wiki/Big_data|3] ([[https://www.ibm.com/blogs/watson-health/the-5-vs-of-big-data/|or 5]]) [[https://en.wikipedia.org/wiki/Big_data|Vs of data science]]: | + | Storage is important in digital pathology. Image data can be subject to any of the [[https://en.wikipedia.org/wiki/Big_data|3]] ([[https://www.ibm.com/blogs/watson-health/the-5-vs-of-big-data/|or 5]]) [[https://en.wikipedia.org/wiki/Big_data|Vs of data science]]: |
| * Variety - Imaging data in pathology is generated during biopsies (macroscopic observations on the sectioning station), brightfield microscopy (high-resolution), immuno observations (multiple channels), and z-stacking. | * Variety - Imaging data in pathology is generated during biopsies (macroscopic observations on the sectioning station), brightfield microscopy (high-resolution), immuno observations (multiple channels), and z-stacking. | ||
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| * Velocity - Data comes in rapidly, with 100s of slides being scanned on a daily basis. This poses challenges in terms of how much pre-treatment and time you can spent on any individual slides. | * Velocity - Data comes in rapidly, with 100s of slides being scanned on a daily basis. This poses challenges in terms of how much pre-treatment and time you can spent on any individual slides. | ||
| + | For these reasons it's important to have tile server solution that is flexible. | ||
| - | + | PMA.core supports the following [[rootdir_config#adding_mounting_points|storage media]]: | |
| + | * local hard disk (think of you conventional ''C:'' and ''D:'' drives and partitions) | ||
| + | * network storage like SMB shares (must be accessible via UNC ''%%\\server\path\to\data%%'' routes) | ||
| + | * [[rootdir_s3|S3-compliant cloud storage]] (Amazon AWS, Western Digital HGST, NetApp, Arvados, IBM...) | ||
| + | * [[rootdir_azure|Microsoft Azure storage]] (including [[rootdir_azure#data_lake_gen2_storage|Data Lake Gen 2]]) | ||
| + | * FTP server (yup, that [[https://www.filezilla.org|free FileZilla File Transfer Protocol server]] is still around and can be now put to new uses for digital pathology applications!) | ||
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| + | Our tile server introduces [[rootdir|root directories]]: virtual mounting points that can point to any of these types of storage, where you have your slides available. | ||
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| + | Most importantly, you can configure your root-directories in a hybrid fashion, with some storage pointing to traditional hard disks, and other (perhaps long term) storage pointing to cloud resources. | ||
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| + | This hybrid configuration model also means you can scale easily over time: you can start with a setup whereby your slides are mostly placed on a (big) local hard disk. After a while, you switch over to your organization's network storage. Even at a later stage, you can transparently migrate to S3-compliant cloud storage. When you have an external collaborator that temporarily wants to share their slide collection with you, you can ask them to setup an FTP server and patch a root-directory through to that one. | ||
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| + | [[rootdir|Root-directory resources]] can have authentication and impersonation information attached to them. In addition, PMA.core has its own [[acl|access control lists]] to determine what [[user_groups]] and [[user_management|individual users]] can see and do (according to [[crud|the CRUD principle]]). | ||
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| + | A comprehensive blog article on the subject of storage and image management is provided at [[https://realdata.pathomation.com|our blog]]. | ||
storage_management.1630408874.txt.gz ยท Last modified: 2021/08/31 14:21 by yves
