supported_file_formats
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supported_file_formats [2022/01/17 14:30] yves [Annotation formats] |
supported_file_formats [2022/02/11 17:41] (current) yves [Whole slide images and virtual slides] |
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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. | 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]]. | 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 |}} | {{::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]]. | 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 |}} | {{::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]]. | 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 |}} | {{: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]]. | 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 |}} | {{::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. | 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 ===== |
| Because a picture says more than a thousand words, oftentimes slides get annotated. Here are some examples: | Because a picture says more than a thousand words, oftentimes slides get annotated. Here are some examples: | ||
| - | * An instructors wants to get a student's attention to a particular area on a slide by drawing arrows in various colors, possibly labeling them | + | * 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 [[CRO|https://en.wikipedia.org/wiki/Contract_research_organization]] 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 [[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 ([[AI/ML/DL|https://en.wikipedia.org/wiki/Machine_learning]]; all of these tools produce annotation layers that need to be integrated for further study and comparison | + | * 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 |
| Pathomation's PMA.core distinguishes between 3 different kinds of annotations: | Pathomation's PMA.core distinguishes between 3 different kinds of annotations: | ||
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| | Third-party | MLD, XML | Yes | No | | | Third-party | MLD, XML | Yes | No | | ||
| - | More information on the [[different kinds of annotations and how they are handled in the Pathomation platform|https://realdata.pathomation.com/annotations-et-al/]] can be found in our [[blog article|https://realdata.pathomation.com/annotations-et-al/]]. | + | 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 ===== |
| - | ======= Miscellaneous ======= | + | Synopic reporting a great way to structure information that was previously largely unstructured. |
| - | ===== Microsoft Excel and CSV ===== | + | 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]]. | ||
| - | ===== Supported Codecs for WSI ===== | + | 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]]. | 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]]. | ||
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| * RLE | * 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]]. | ||
supported_file_formats.1642419001.txt.gz · Last modified: 2022/01/17 14:30 by yves
