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--- supported_file_formats [2021/06/28 17:15] – yves
+++ supported_file_formats [2022/02/11 15:41] (current) – [Whole slide images and virtual slides] yves
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-====== Whole slide images and virtual slides =====
+===== Whole slide images and virtual slides =====
 PMA.core supports a variety of image capturing techniques and modalities.
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 You can read more about our philosophy regarding the support of vendor-specific file format [[https://www.prweb.com/releases/pathomation_announces_the_support_for_five_new_digital_pathology_file_formats_including_philips_isyntax/prweb17933169.htm|in our press release]].
-===== Brightfield =====
+An introduction discussing the file format //issue// in digital pathology is available through the [[https://www.digitalpathologytoday.com/episodes/s2e17|Digital Pathology Today podcast]].
+==== Brightfield ====
 {{::format_brightfield.png?nolink&200 |}}
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 A full up-to-date list is available on our website at [[https://www.pathomation.com/formats|https://www.pathomation.com/formats]].
-===== Fluorescence =====
+==== Fluorescence ====
 {{::format_fluo.png?nolink&200 |}}
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 An up-to-date list of supported fluorescent file formats is available on our website at [[https://www.pathomation.com/formats|https://www.pathomation.com/formats]].
-===== Z-stacking =====
+==== Z-stacking ====
 {{:format_zstack.png?nolink&200 |}}
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 An up-to-date list of z-stacking formats supported by PMA.core is available on our website at [[https://www.pathomation.com/formats|https://www.pathomation.com/formats]].
-===== Time series =====
+==== Time series ====
 {{::format_time_series.png?nolink&200 |}}
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 Recently we've added support for these time-series data. We don't have too much reference datasets yet though, so if you have use cases for these, do [[https://www.pathomation.com/contact|let us know]]. We can then work with you to find the most optimum way of presenting these to further your specific (research) project.
-======= Annotation formats =======
+===== Annotation formats =====
-======= Forms and meta-data =======
+Because a picture says more than a thousand words, oftentimes slides get annotated. Here are some examples:
-======= Miscellaneous =======
+  * 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
-===== Microsoft Excel and CSV =====
+Pathomation's PMA.core distinguishes between 3 different kinds of annotations:
-===== Supported Codecs for WSI =====
+^ 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 =====
+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]].
+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 =====
+==== 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, [[https://www.pathomation.com/contact|let us know]] 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 ====
+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]].
+==== Troubleshooting ====
+See [[format_troubleshoot|our separate section]].