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supported_file_formats [2022/01/17 12:37] – [Forms and meta-data] yvessupported_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. 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:
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-======= Forms and meta-data =======+===== Forms and meta-data =====
  
 Synopic reporting a great way to structure information that was previously largely unstructured. Synopic reporting a great way to structure information that was previously largely unstructured.
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 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". 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 [[specific section on the subject in this wiki|forms]].+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 [[our blog article|https://realdata.pathomation.com/how-to-handle-slide-meta-data/]]. +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...
  
-===== Supported Codecs for WSI =====+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.1642419444.txt.gz · Last modified: by yves
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