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pma_python

pma_python is a Python wrapper library for PMA.start (http://free.pathomation.com), a universal viewer by Pathomation for whole slide imaging and microscopy.

YOU NEED TO HAVE PMA.START (OR PMA.CORE) RUNNING IN ORDER TO USE THIS LIBRARY. PMA_PYTHON IS NOT A STAND-ALONE LIBRARY FOR WSI.

If you're working with

  • microscopy data and are you tired of having to use a different library for each vendor specific digital slide format
  • 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)

and you're doing all of this in Python, then PMA.start and pma_python are for you!

PMA.start can be downloaded free of charge from http://free.pathomation.com

With pma_python, 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 bring it all into Python now.

The following vendor formats are currently supported:

  • TIFF (.tif, .tiff) with JPEG, JPEG2000, LZW, Deflate, Raw, RLE
  • JPEG (.jpeg, .jpg)
  • JPEG 2000 (.jp2)
  • PNG (.png)
  • Olympus VSI (.vsi) with lossless JPEG, JPEG, Raw
  • Ventana / Roche BIF (.bif)
  • Hamamatsu (.vms, .ndpi, .dcm) with JPEG, JPEG2000
  • Huron Technologies (.tif)
  • 3DHistech (.mrxs) with JPEG, PNG, BMP
  • Aperio / Leica (.svs, .cws, .scn, .lif, DICOMDIR) with JPEG, JPEG2000
  • Carl Zeiss (.zvi, .czi, .lsm) with Raw, PNG, JPEG, LZW, Deflate, JPEG2000
  • Open Microscopy Environment OME-TIFF (.tf2, .tf8, .btf, .ome.tif)
  • Nikon (.nd2, .tiff) with Deflate, JPEG, JPEG2000, LZW, Deflate, Raw, RLE
  • Philips (.tif) with JPEG, JPEG2000, LZW, Deflate, Raw, RLE
  • Sakura (.svslide) with JPEG(sqlite2, sqlite3, mssql)
  • Menarini (.ini) with Raw
  • Motic (.mds)
  • Zoomify (.zif) with JPEG, JPEG2000, LZW, Deflate, Raw, RLE
  • SmartZoom (.szi) with JPEG, BMP
  • Objective Imaging / Glissano (.sws)
  • Perkin Elmer (.qptiff)

The most up to date list with supported file formats can be found at http://free.pathomation.com/formats

Installation from source

To install from pypi

pip install pma_python

To upgrade an already existing version from pypi

pip install --upgrade pma_python

How to use

>>> from pma_python import *

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Python wrapper library for PMA.start, a universal viewier for whole slide imaging and microscopy

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