supported_file_formats
Differences
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supported_file_formats [2022/02/11 17:41] yves [Whole slide images and virtual slides] |
supported_file_formats [2023/01/17 17:03] (current) yves [Fluorescence] |
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| An introduction discussing the file format //issue// in digital pathology is available through the [[https://www.digitalpathologytoday.com/episodes/s2e17|Digital Pathology Today podcast]]. | An introduction discussing the file format //issue// in digital pathology is available through the [[https://www.digitalpathologytoday.com/episodes/s2e17|Digital Pathology Today podcast]]. | ||
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| + | ==== Grossing and macroscopic ==== | ||
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| + | {{::format_macro_gross.png?nolink&200 |}} | ||
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| + | Gross processing or "grossing" is the process by which pathology specimens undergo examination with the bare eye to obtain diagnostic information, as well as cutting and tissue sampling in order to prepare material for subsequent microscopic examination. ([[https://en.wikipedia.org/wiki/Gross_processing|Wikipedia]]) | ||
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| + | In order to provide a reference and link between macroscopic and microscopic samples, a //regular// photograph is often taken from a specimen before it is [[https://en.wikipedia.org/wiki/Histology#Sample_preparation|further processed]]. | ||
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| + | PMA.core supports [[https://www.pathomation.com/formats|common file formats like JPG, JPEG, JP2, TIFF, TIF, PNG, and others]] to support this kind of observations and incorporate them seamlessly in digital pathology applications and workflows. | ||
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| ==== Brightfield ==== | ==== Brightfield ==== | ||
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| {{::format_fluo.png?nolink&200 |}} | {{::format_fluo.png?nolink&200 |}} | ||
| - | DAPI, Cy3, Cy5, ... If these terms sound familiar, changed are you're engaged in fluorescent microscopy. We've been working with many vendors throughout the years to optimally support this imaging type. You can toggle individual channels directly in PMA.core, and do histogram clipping as you see fit. Advanced downstream application (that run on top of PMA.core) like [[https://www.pathomation.com/pma.studio|PMA.studio]] can even visualize the histogram of each channel for you, and apply additional per-channel gamma correction. | + | DAPI, Cy3, Cy5, ... If these terms sound familiar, changed are you're engaged in fluorescent microscopy. We've been working with many vendors throughout the years to optimally support this imaging type. You can toggle individual channels directly in PMA.core, and do [[fluo#histogram_clipping|histogram clipping]] as you see fit. Advanced downstream application (that run on top of PMA.core) like [[https://www.pathomation.com/pma.studio|PMA.studio]] can even visualize the histogram of each channel for you, and apply additional per-channel gamma correction. |
| 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]]. | ||
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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 [[forms|specific section on the subject in this wiki]]. | + | PMA.core supports this kind of data capture and the ability to generate forms. For more information, see the [[form_management|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]]. | 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]]. | ||
supported_file_formats.1644590465.txt.gz ยท Last modified: 2022/02/11 17:41 by yves
