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supported_file_formats [2021/07/13 12:43] yves |
supported_file_formats [2022/01/17 14:53] yves [Supported Codecs for WSI] |
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======= Annotation formats ======= | ======= Annotation formats ======= | ||
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+ | Because a picture says more than a thousand words, oftentimes slides get annotated. Here are some examples: | ||
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+ | * An instructor wants to get a student's attention to a particular area on a slide by drawing arrows in various colors, possibly labeling them | ||
+ | * A [[https://en.wikipedia.org/wiki/Contract_research_organization|CRO]] has its pathologists annotate slides for specific types of tissue like necrotic or tumor tissue. The pathologists do this according to a pre-determined color scheme | ||
+ | * A pharma company employs various types of image analysis tools ([[https://en.wikipedia.org/wiki/Machine_learning|AI/ML/DL]]; all of these tools produce annotation layers that need to be integrated for further study and comparison | ||
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+ | Pathomation's PMA.core distinguishes between 3 different kinds of annotations: | ||
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+ | |||
+ | ^ Annotation type ^ Format examples ^ Can read ^ Can write ^ | ||
+ | | Native | MRXS, NDPI(A), SVS | Yes | No | | ||
+ | | PMA.core | WKT | Yes | Yes | | ||
+ | | Third-party | MLD, XML | Yes | No | | ||
+ | |||
+ | More information on the [[https://realdata.pathomation.com/annotations-et-al/|different kinds of annotations and how they are handled in the Pathomation platform]] can be found in our [[https://realdata.pathomation.com/annotations-et-al/|blog article]]. | ||
+ | |||
======= Forms and meta-data ======= | ======= Forms and meta-data ======= | ||
+ | Synopic reporting a great way to structure information that was previously largely unstructured. | ||
+ | |||
+ | Here's a example: instead of letting a pathologist write a report in which he says that the patient's tissue shows signs of abnormally proliferating cell groups, you let him or her fill out a form with a checkbox for "TumorTissuePresent". | ||
+ | |||
+ | PMA.core supports this kind of data capture and the ability to generate forms. For more information, see the [[forms|specific section on the subject in this wiki]]. | ||
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+ | Of course PMA.core isn't the only tool in the world that can do this. We acknowledge that by providing various options to integrate external meta-data into PMA.core as well. For more information on that subject, we refer to [[https://realdata.pathomation.com/how-to-handle-slide-meta-data/|our blog article]]. | ||
======= Miscellaneous ======= | ======= Miscellaneous ======= | ||
===== Microsoft Excel and CSV ===== | ===== Microsoft Excel and CSV ===== | ||
+ | {{::export_to_excel_2.png?200 |}}In PMA.core, much information is presented in the form of a list: users, slides, forms... | ||
+ | |||
+ | No matter how extended we make these list interfaces however, there's going to be a time where you think "well, if I only could re-format it like _this_, of if I could just send it off to _that_ lady... | ||
+ | |||
+ | Most views in PMA.core therefore have an Excel export button in the top-right corner that allow you to export the current data as list. Go ahead and try it, and if you don't find what you're looking for, [[let us know|https://www.pathomation.com/contact]] so we can incorporate it in the next version (no promises; we'll still have to evaluate the extend to which your request would be a useful feature to have for our entire user base). | ||
===== Supported Codecs for WSI ===== | ===== Supported Codecs for WSI ===== | ||
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The word Codec is a combination of two words "coder" and "decoder". A piece of each word is used to create the commonly used word "Codec". [[https://en.wikipedia.org/wiki/Codec|Think of this as both a coder and decoder]]. | The word Codec is a combination of two words "coder" and "decoder". A piece of each word is used to create the commonly used word "Codec". [[https://en.wikipedia.org/wiki/Codec|Think of this as both a coder and decoder]]. | ||
+ | Coding and decoding images is required to convert pixels into bits of information and ROIs that can be transmitted, and translated. | ||
+ | PMA.core currently supports the following codecs and data encoding standards: | ||
+ | * Blosc | ||
+ | * BMP | ||
+ | * Deflate | ||
+ | * iSyntax | ||
+ | * JPEG | ||
+ | * JPEG2000 | ||
+ | * JPEGXR | ||
+ | * lossless | ||
+ | * LZW | ||
+ | * PNG | ||
+ | * RLE | ||
+ | More and up-to-date information on how this applies to specific file formats can be found at [[https://www.pathomation.com/formats|our website]]. | ||