PMA.core 3.0.3

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===== Whole slide images and virtual slides =====

PMA.core supports a variety of image capturing techniques and modalities.

A full list of currently supported formats is available at [[https://www.pathomation.com/formats|https://www.pathomation.com/formats]].

You can read more about our philosophy regarding the support of vendor-specific file formats [[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]].

An introduction discussing the file format //issue// in digital pathology is available through the [[https://www.digitalpathologytoday.com/episodes/s2e17|Digital Pathology Today podcast]].

==== Grossing and macroscopic ====

{{::format_macro_gross.png?nolink&200 |}}

Gross processing or "grossing" is the process by which pathology specimens undergo examination with the naked 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]])

In order to provide a reference and link between macroscopic and microscopic samples, a //regular// photograph is often taken of a sample before it is [[https://en.wikipedia.org/wiki/Histology#Sample_preparation|further processed]].

PMA.core supports [[https://www.pathomation.com/formats|common file formats like JPG, JPEG, JP2, TIFF, TIF, PNG, and others]] to support these observations and incorporate them seamlessly in digital pathology applications and workflows.

==== Brightfield ====

{{::format_brightfield.png?nolink&200 |}}

PMA.core's slide reading engine supports over 35 different vendor-specific file formats that are used to encapsulate brightfield microscopy data. We offer a mix of open source community formats ([[https://www.openmicroscopy.org|OMERO TIFF & ZARR]], [[https://www.dicomstandard.org/|[DICOM]], ...), as well as legacy ones such as Olympus Webview.

A full up-to-date list is available on our website at [[https://www.pathomation.com/formats|https://www.pathomation.com/formats]].

==== Fluorescence ====

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DAPI, Cy3, Cy5, ... If these terms sound familiar, chances 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 applications 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]].

==== Z-stacking ====

{{:format_zstack.png?nolink&200 |}}

Both brightfield and fluorescent slides are often generated on a [[https://en.wikipedia.org/wiki/Microtome|microtome]], which results in smooth, flat surfaces. However, when [[https://en.wikipedia.org/wiki/Cytopathology|working with cytological samples]], or doing microscopy in crop research, this is not always the case. Smears and similar materials are typically captured through z-stacking, whereby [[https://en.wikipedia.org/wiki/Focus_stacking#In_microscopy|a sample is traversed in miniscule steps of one or two micron at the time]].

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 ====

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Say that you want to observe a cell culture or embryo development over a period of 24 hours. Some manufacturers allow capturing all the data from that time period in a single container (possible in combination with other dimensions like the above-mentioned).

Recently we've added support for these time-series data. We don't have many reference datasets yet, 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 optimal way of presenting these to further your specific (research) project.

===== Annotation formats =====

Because a picture says more than a thousand words, oftentimes slides get annotated. Here are some examples:

  * An instructor wants to draw students' attention to a particular area on a slide by drawing arrows in various colors, with the possibility of 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

Pathomation's PMA.core distinguishes between 3 different kinds of annotations:


^ 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 unstructured (from a database perspective).

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 [[form_management|specific section on this subject in the 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/|one of our blog articles]].
===== Miscellaneous =====

==== Microsoft Excel and CSV ====

{{::export_to_excel_2.png?200 |}}In PMA.core, a lot of 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_, or 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 a 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 extent 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]].
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