Opening Files

Quick Start

Where possible, pims detects the type of file(s) automatically. Here are some examples.

import pims
images = pims.open('my_directory/*.png')  # many PNGs with sequential names
images = pims.open('my_directory/*.tif')  # many TIFs with sequential names
images = pims.open('tiff_stack.tif')  # one TIF file containing many frames

If your images are in a color format, but you need to convert them to greyscale for processing, you can use pims.as_grey:

import pims
images = pims.as_grey(pims.open('my_directory/*.png'))

as_grey operates on any PIMS reader object, and it only converts images as they are loaded. PIMS makes it easy to create your own custom functions like this, called Pipelines.

Using Specific Readers

PIMS has several built-in readers. If you don’t want to use open to dispatch to them automatically, you can use them directly. For example:

import pims
images = pims.ImageSequence('my_directory/*.png')

The main readers are:

• ImageSequence

• TiffStack

• Video

• Bioformats

See their individual pages for details.

If you have a file format not yet supported by PIMS, it is easy to define your own reader and get PIMS lazy-loading and slicing behavhior “for free.” See Custom Readers.