ome / bio-formats-documentation Goto Github PK

View Code? Open in Web Editor NEW

8.0 11.0 15.0 9.54 MB

Bio-Formats documentation

Home Page: https://www.openmicroscopy.org/bio-formats/

License: BSD 2-Clause "Simplified" License

Java 76.72% HTML 1.13% Python 21.77% Makefile 0.11% CSS 0.27%

bio-formats documentation

bio-formats-documentation's Introduction

Bio-Formats

Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats.

If you are having an issue with Bio-Formats and need support, please see the support page.

Purpose

Bio-Formats' primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format. See About Bio-Formats for further information.

Supported formats

Bio-Formats supports more than a hundred file formats.

For users

Many software packages use Bio-Formats to read and write microscopy formats.

For developers

You can use Bio-Formats to easily support these formats in your software.

More information

For more information, see the Bio-Formats web site.

Pull request testing

We welcome pull requests from anyone, but ask that you please verify the following before submitting a pull request:

verify that the branch merges cleanly into develop
verify that the branch compiles with the clean jars tools Ant targets
verify that the branch compiles using Maven
verify that the branch does not use syntax or API specific to Java 1.8+
run the unit tests (ant test) and correct any failures
test at least one file in each affected format, using the showinf command
internal developers only: run the data tests against directories corresponding to the affected format(s)
make sure that your commits contain the correct authorship information and, if necessary, a signed-off-by line
make sure that the commit messages or pull request comment contains sufficient information for the reviewer(s) to understand what problem was fixed and how to test it

bio-formats-documentation's People

Contributors

Stargazers

Watchers

Forkers

snoopycrimecop hflynn sbesson dgault melissalinkert kouichi-c-nakamura jburel kennethgillen mtbc joshmoore atarkowska manics knabar will-moore

bio-formats-documentation's Issues

Building of examples

see: gh-3 specifically,

Primary goal being that any examples which appear in the docs should be regularly tested.

Third-party tools additions

Potential candidate for adding to the list of third-party tools consuming Bio-Formats https://docs.openmicroscopy.org/bio-formats/latest/users/index.html

R - https://github.com/aoles/RBioFormats
Wolfram (incl. Mathematica) - https://github.com/WolframResearch/BioFormatsLink

Add configuration option to validate against local ome-model docs

When building against a SNAPSHOT build of ome-model, there are no public deployed docs to validate against. Add a maven property to allow validation against a local directory containing the docs (i.e. bio-formats-build/ome-model/...)

Bump cdm version in the documentation

Following ome/bioformats#3788, https://docs.openmicroscopy.org/bio-formats/6.9.1/developers/java-library.html should be adjusted accordingly /cc @jburel

This raises once more the question of whether the dependency list could be generated automatically into a format that can be simply included in the rST sources.

bfsave not generating an output Tif-file

Hi,

In MATLAB, I'm trying to convert an m-pixel by n-pixel by k-channel matrix to a multichannel image in a Tiff format using bfsave() function.

a code snippet:
path_file = char("A:\taliaha\Matched Slices\Tiff_Data\" + dataset_name + ".tif"); bfsave(m_dataset, path_file)

The code produces no exception message, however, no file is generated in the specified location.

Any advice?

Thanks,

Dean

MRC format: clarify ownership and support

While reviewing ome/bioformats#3975, I came across our documentation page at https://bio-formats.readthedocs.io/en/stable/formats/mrc.html and this raised a few questions.

The MRC file format history is complex. As indicated in the linked Wikipedia page, it was originally developed by the MRC-LMB (hence the name), has been extended to support electron cryo-microscopy. Its maintenance migrated to the CCP-EM project and there are a few extensions of the CCP-EM MRC standard including the version generated by IMOD which is linked from the documentation.

We should probably amend the documentation page to reflect the current status of the development/ownership of the format and clarify the modes which are expected to be supported by the Bio-Formats reader.

Building of examples

see: gh-3 specifically,

Primary goal being that any examples which appear in the docs should be regularly tested.

Broken NIFTI links

The NIFTI links have been broken in the linkcheck tests for a while now: https://nifti.nimh.nih.gov/nifti-1/

So far I haven't been able to find a suitable alternative. @melissalinkert do you have any suggestions for alternative links?

Post decoupling content updates

See ome/bioformats#3117. As this repository is currently scheduled to become the new location for the Bio-Formats documentation from 5.8.2, content on a few pages will require some adjustments before moving to production:

http://docs.openmicroscopy.org/bio-formats/5.8.1/developers/building-bioformats.html probably requires an update since the documentation will be built separately
http://docs.openmicroscopy.org/bio-formats/5.8.1/developers/components.html will need updates to document the new decoupled components (examples and documentation)
http://docs.openmicroscopy.org/bio-formats/5.8.1/developers/format-documentation.html will need a review since these pages are now auto-generated.
http://docs.openmicroscopy.org/bio-formats/5.8.1/developers/useful-scripts.html could drop the sphinx mention

Review dependency list

@chris-allan pointed out that https://docs.openmicroscopy.org/bio-formats/6.6.0/developers/java-library.html#dependencies lists all the dependencies across all components of the Bio-Formats repository while the text above refers to using formats-gpl and all dependencies.

The rationale for updating it is that this list currently includes log4j as a dependency of the deprecated loci_tools bundle (which is scheduled to be dropped in the next release as part of https://www.openmicroscopy.org/security/advisories/2021-SV4/). Other items like imagej which is a dependency of the bio-formats-plugins component are also confusing if the intent is just to use formats-gpl

For the next release this list should likely be limited to the third-party dependencies of the formats-gpl component only.

Convert several timepoints and/or channels at the same time

Hi,

Thanks for the nice tool.

I just discovered the -timepoint and -channel arguments. Is it possible to convert more than one timepoint at once to have a timelapse as output but not all the timepoints of the orginal .vsi file (to convert to .tif in my case)?

Cheers,
Mathieu

Getting error 'Unsupported major.minor version 52.0' using bioformats command line tools

I am trying to use bio-formats in general and right now bio-formats command line tools. Whenever I run a tool (bfconvert for example), I am getting the error:

Exception in thread "main" java.lang.UnsupportedClassVersionError: loci/formats/tools/ImageConverter : Unsupported major.minor version 52.0

I am on macOS Mojave (10.14.3).

The tutorial on using command line tools looks deceptively simple and mentions how java is now bundled in the downloaded zip? Ok, great. HOw do I get it to work?

I tried to download/install the recent Java from Oracle but that did not solve the issue?