bioformats | Java library for reading and writing data | Computer Vision library

by ome Java Version: v6.13.0 License: GPL-2.0

X-Ray Key Features Code Snippets Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | bioformats Summary

bioformats is a Java library typically used in Artificial Intelligence, Computer Vision applications. bioformats has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

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Quality

Security

License

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Support

bioformats has a low active ecosystem.

It has 323 star(s) with 240 fork(s). There are 29 watchers for this library.

It had no major release in the last 12 months.

There are 175 open issues and 221 have been closed. On average issues are closed in 385 days. There are 17 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of bioformats is v6.13.0

Quality

bioformats has 0 bugs and 0 code smells.

Security

bioformats has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

bioformats code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

bioformats is licensed under the GPL-2.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

bioformats releases are available to install and integrate.

Build file is available. You can build the component from source.

It has 165701 lines of code, 7841 functions and 731 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed bioformats and discovered the below as its top functions. This is intended to give you an instant insight into bioformats implemented functionality, and help decide if they suit your requirements.

Initialize the file
Parses a key and value pair
Iterate through ND2 meta attributes and store them in an array
Populate metadata store
Gets the companion file
Finds the key value pair that matches one of regular expressions
Split the metadata into tokens
Internal method for defining a slidebook
Returns true if the given offset is within the pixel offset
The main interface
Gets the Tiff reader
Make sure that the data files are valid
Look for files that have a similar location
Initialize the LIFF file
Internal method used to initialize the format
Initialize HTML companion file
Reads and parses the XML file
Initialize data structures
Process an element
Set the ID
Initialize the OME - XML file
This method is used internally to initialize a NFD file
Implementation of this class
Initializes a temporary file
Initializes the xce file
Initialization method

Get all kandi verified functions for this library.

bioformats Key Features

No Key Features are available at this moment for bioformats.

bioformats Examples and Code Snippets

No Code Snippets are available at this moment for bioformats.

Community Discussions

Trending Discussions on bioformats

AWS Lambda and S3: passing s3 object path to image process function

Bioformats-Python error: 'ascii' codec can't encode character u'\xb5' when using OMEXML()

python setup.py egg_info failed when installing python-bioformats

QUESTION

AWS Lambda and S3: passing s3 object path to image process function

Asked 2019-May-03 at 00:28

My intention is to have a large image stored on my S3 server and then get a lambda function to read/process the file and save the resulting output(s). I'm using a package called python-bioformats to work with a proprietary image file (which is basically a whole bunch of tiffs stacked together). When I use

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ANSWER

Answered 2019-May-03 at 00:28

If your bioformats.get_omexml_metadata() function requires a filepath as an argument, then you will need to have the object downloaded before calling the function.

This could be a problem in an AWS Lambda function because there is a 500MB limit on available disk space (and only in /tmp/).

If the data can instead be processed as a stream, you could read the data as it is required without saving to disk first. However, the python-bioformats documentation does not show this as an option. In fact, I would be surprised if your above code works, given that it is expecting a path while imageobj is the contents of the file.

Source https://stackoverflow.com/questions/55961759

QUESTION

Bioformats-Python error: 'ascii' codec can't encode character u'\xb5' when using OMEXML()

Asked 2017-Apr-26 at 12:01

I am trying to use bioformats in Python to read in a microscopy image (.lsm, .czi, .lif, you name it), print out the meta data, and display the image. ome = bf.OMEXML(md) gives me an error (below). I think it's talking about the information stored within md. It doesn't like that the information in md isn't all ASCII. But how do I overcome this problem? This is what I wrote:

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ANSWER

Answered 2017-Apr-26 at 12:01

Thank you for adding the sample image. That helped tremendously!

Let's first remove all the unnecessary Tkinter code until we get to a Minimal, Complete and Verifiable Example that allows us to reproduce your error message.

Source https://stackoverflow.com/questions/43598709

QUESTION

python setup.py egg_info failed when installing python-bioformats

Asked 2017-Mar-30 at 21:08

I am working on Ubuntu 16.04, and I have installed virtualenvs. I am in one env and trying to install python-bioformats The installation instruction form the official website just indicate to install as:

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ANSWER

Answered 2017-Mar-30 at 21:08

The problem is that you have note installed Java. You need to install Java on you system. If you think it is installed, then sure it is not on the Linux's paths to search for executables and you need to add the path to Java to environment variable PATH. Whenever you have Java installed/add to Linux's PATH then execute type -p java on command line and it should return the path to the java executable.

Source https://stackoverflow.com/questions/43126723

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install bioformats

You can download it from GitHub.
You can use bioformats like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the bioformats component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .