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PMA.start – free whole slide image viewer

A digital pathology viewer by Pathomation

Are you working with

  • microscopy data and are you tired of having to use a different viewer for each vendor specific digital slide format?
  • ImageJ (or FIJI) and whole slide imaging data and find it cumbersome having to take snapshot or export / import TIFF images all the time?
  • Image analysis software and are you looking for a way to have complete control over your algorithms (and not just be able to select those provided for you)?
  • Novel evaluation methods for histology / pathology and do you just wish there was a way to now automatically evaluate it on 100s of slides (batch processing)?

Then PMA.start is for you!

What can you do with Pathomation’s free digital pathology software?

After installation, you can inspect and navigate any type of microscopic imaging file format available. Whether you have macroscopic observations, whole slide imaging data, or fluorescent snapshot observations, we can display it all in a single easy to browse environment. Through our ImageJ (or FIJI) plugin, you can bring any type of microscopic imaging data into one of the most widely used image analysis programs on the market. Utilizing our powerful webservice API you can automate your image analysis workflows via scripting and use any image processing library you want.

Digital slide viewer
PMA.start whole slide image viewer

Fluorescent whole slide image
Multi channel fluorescent whole slide image

Supported whole slide image file formats

 

Format Image File Extension
TIFF .tif, .tiff Supported
JPEG .jpeg, .jpg Supported
JPEG 2000 .jp2 Supported
PNG .png Supported
Olympus VSI .vsi Supported
Ventana / Roche BIF .bif Supported
Hamamatsu NDPI .ndpi Supported
Hamamatsu DICOM .dcm Supported
Huron Technologies .tif Supported
3DHistech MRXS .mrxs Supported
Aperio / Leica SVS .svs Supported
Leica SCN .scn Supported
Leica DICOM Sup145 DICOMDIR Supported
Carl Zeiss ZVI .zvi Supported
Carl Zeiss CZI .czi Supported
Carl Zeiss Laser Scanning Microscopy .lsm Supported
Open Microscopy Environment OME-TIFF .tf2, .tf8, .btf Supported
Nikon ND2 .nd2 Supported
Nikon TIFF .tif, .tiff Supported
Philips TIFF .tif Supported
Sakura SVSlide .svslide Supported
Menarini DSight RAW .ini Supported
Motic .mds Supported
Zoomify .zif Supported

Features

  • View microscopy data from different origins without having to switch to a new viewer for each vendor-specific format
  • Integration with ImageJ (or FIJI) for convenient image analysis experiments
  • Set up automatic image processing workflows through an open Application Programming Interface (API)

Pathomation’s free software offering is a client/server software solution that consists of two components:

PMA.start is a free web based whole slide image viewer, built using Javascript, HTML and CSS, that

  • interacts with a locally installed instance of PMA.core.lite
  • efficiently allows navigation of giga-pixel imaging data
  • can visualize both brightfield and fluorescent data
  • allows channel-selection for fluorescent imaging data

PMA.core.lite is a locally installed server application, built using Microsoft .Net framework, that

Our platform also makes use of various 3rd party software libraries all of which are listed here.

Presentation at the Computational Pathology Workshop, Den Haag, Netherlands 2016

How to cite

We currently don’t have a citation for our software. An application note for bioinformatics is in the works, but lack of time has prevented me pushing this forward.

We’d be very pleased if you could reference PMA.start through its public URL at http://free.pathomation.com in your work. A formal citation for this is:

Sucaet Yves, Pappas Angelos and Wim Waelput. “Free Whole Slide Image Viewer – PMA.Start | Universal Digital Microscopy Software”. http://free.pathomation.com/ . 2017. Web. {DD-MMM-YYYY}.

If this concerns a paper, we’d love to hear about it once it’s in press, so we can start building a “projects that use PMA.start” page on our website.