python-bioformats | Read and write life sciences file formats

by CellProfiler Python Version: 4.0.7 License: Non-SPDX

X-Ray Key Features Code Snippets(2)Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | python-bioformats Summary

python-bioformats is a Python library. python-bioformats has no bugs, it has no vulnerabilities, it has build file available and it has low support. However python-bioformats has a Non-SPDX License. You can install using 'pip install python-bioformats' or download it from GitHub, PyPI.

Read and write life sciences file formats

Support

Quality

Security

License

Reuse

Support

python-bioformats has a low active ecosystem.

It has 81 star(s) with 39 fork(s). There are 16 watchers for this library.

It had no major release in the last 12 months.

There are 54 open issues and 43 have been closed. On average issues are closed in 211 days. There are 4 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of python-bioformats is 4.0.7

Quality

python-bioformats has 0 bugs and 0 code smells.

Security

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

python-bioformats code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

python-bioformats has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

python-bioformats releases are available to install and integrate.

Deployable package is available in PyPI.

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

Top functions reviewed by kandi - BETA

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

Create an image reader class
Creates an io formatReader class
Return a class list
Get the version number
Make a reader class
Make a loci class
Get an image reader
Release an image reader
Close the stream
Set the roi count
Return the qualified name for a namespace tag
Create an image writer class
Makes a class suitable for logging
Sets the pixel dimensions of the image
Return a dictionary of namespaces
Create StructuredAnnotations element
Sets the channel s samples per pixel
Wrap a MetadataStore object
Get omero credentials
Make a text node
Sets the big endian of the image
Makes a loci FormatTools class
Make a writer class for the given class_name
Make a reader wrapper for the given class_name
Create an OMERO reader instance
Creates a new pixel type
Makes an OM - TIFF writer class
Download a file

Get all kandi verified functions for this library.

python-bioformats Key Features

No Key Features are available at this moment for python-bioformats.

python-bioformats Examples and Code Snippets

Apply openCV-python adaptive threshold to 3D tiff

Python

Lines of Code : 23

License : Strong Copyleft (CC BY-SA 4.0)

Copy

import javabridge
import bioformats

javabridge.start_vm(class_path=bioformats.JARS)

path_to_data = '/path/to/data/file_name.tif'

xml_string = bioformats.get_omexml_metadata(path_to_data)
ome = bioformats.OMEXML(xml_string) # be sure eve

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

Python

Lines of Code : 23

License : Strong Copyleft (CC BY-SA 4.0)

Copy

import javabridge as jv
import bioformats as bf

jv.start_vm(class_path=bf.JARS, max_heap_size='12G')

file_full_path = '/path/to/Cell1.lsm'

md = bf.get_omexml_metadata(file_full_path)

ome = bf.OMEXML(md)

jv.kill_vm()

Community Discussions

Trending Discussions on python-bioformats

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

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

...

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

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:

...

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 python-bioformats

You can install using 'pip install python-bioformats' or download it from GitHub, PyPI.
You can use python-bioformats like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

Find more information at: