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scifio-tutorials's Introduction

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SCIFIO (SCientific Image Format Input & Output) is an extensible Java framework for reading and writing images, particularly N-dimensional scientific images.

This core package supports parsing pixels and metadata for a collection of open formats. Additional formats can be supported simply by downloading SCIFIO plugins and including them in your project.

Purpose

SCIFIO's primary purpose is to provide a clear convention for supporting image input and output. By lowering the barrier for adding new image formats, all SCIFIO-backed software will grow more versatile and powerful.

Supported formats

The SCIFIO core includes support for:

  • APNG
  • AVI
  • BMP
  • DICOM
  • EPS
  • FITS
  • GIF
  • ICS
  • JPEG
  • JPEG2000
  • MNG
  • Micro-Manager
  • NRRD
  • PCX
  • PGM
  • QuickTime
  • TIFF
  • Zipped images

Additionally, Bio-Formats is available as a SCIFIO plugin for supporting more than a hundred additional proprietary formats.

For users

ImageJ2 and Fiji use SCIFIO for image I/O.

For developers

Several software libraries use SCIFIO for image I/O:

  • SCIFIO has built-in support for opening and saving ImgLib2 data structures (see the io.scif.img package).
  • We have updated Bio-Formats to also support SCIFIO plugins, backwards compatibly with existing code.
  • ITK has an ImageIO module for reading and writing images using SCIFIO.

Developer documentation:

More information

For more information, see the SCIFIO FAQ and SCIFIO web site.

Getting help

SCIFIO uses the Image.sc Forum for support. Start a new topic tagged with scifio.

Contributing to SCIFIO

SCIFIO is an open project and anyone is very welcome to submit pull requests to the SCIFIO repository.

With SCIFIO's focus on extensibility, you typically will not need to make upstream changes to get your formats into users' hands. However, if you are interested in submitting a pull request, that's great! All we ask is that you check:

mvn clean test

from the top level.

If you're adding a new feature, it would be fantastic if you could write a unit test for it! Simply base it on JUnit to have it run by the SCIFIO test suite.

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scifio-tutorials's Issues

Add a tutorial on how to use the TIFF classes

From a thread on forum.image.sc:

But build and write of a standard Tiff file should be possible, as there are lots of TIFF classes in the io.scif.media.imageio.plugins.tiff. library? And GeoTiff is just Tiff Standard Version 6 plus some additional, geo-specific tags.

Hence, question without Geo would be: But which classes are needed (Writer, TIFFSaver, โ€ฆ?) to construct and write a Tiff file? How to build the dataset and tag entities and save them as a Tiff file?

Create "Advanced" tutorials

Would be nice to create some tutorials to highlight the features of SCIFIO that stand out, e.g. compared to Bio-Formats.

Some ideas for this series of tutorials:

  • Modifying reader behavior via filters
  • Configuration through high-level API via SCIFIOConfig
  • Opening a large dataset and manipulating the planes, using caching

Exception in T1cReadingTilesGood

I'm trying to use T1cReadingTilesGood with a real image, using SCIFIO 0.27.1. I changed the hugeImage variable to the pathname of a tiled TIFF image. When I run it, I get an exception:

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 2
at io.scif.util.FormatTools.checkTileSize(FormatTools.java:671)
at io.scif.util.FormatTools.checkPlaneForWriting(FormatTools.java:647)
at io.scif.util.FormatTools.checkPlaneForReading(FormatTools.java:632)
at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:610)
at io.scif.formats.MinimalTIFFFormat$Reader.openPlane(MinimalTIFFFormat.java:537)
at io.scif.AbstractReader.openPlane(AbstractReader.java:150)
at io.scif.AbstractReader.openPlane(AbstractReader.java:52)
at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:225)
at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:191)
at T1cReadingTilesGood.main(T1cReadingTilesGood.java:96)

This is on the first iteration of the inner for loop. The arguments passed to openPlane() are 0, 0, { 0,0 }, { 128, 128 }.

The same ArrayIndexOutOfBoundsException happens with every type of image I try, though the stack trace differs.

Better explain planar/non-planar axes

I think this concept is very confusing, as the phrase "planar axis" conveys an idea of "contributing to plane count" to many people. At the least it a there should be a good tutorial explaining this distinction and why it is this way (abstraction that was necessary to handle interleaved/non-interleaved/non-planar Channel scenarios)

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