Universal viewing of digital microscopy, whole slide imaging and digital pathology data
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)
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
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
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