| Name | bfio JSON |
| Version |
2.0.5
JSON |
| download |
| home_page | |
| Summary | Simple reading and writing classes for tiled tiffs using Bioformats. |
| upload_time | 2021-02-23 17:55:48 |
| maintainer | |
| docs_url | None |
| author | Nick Schaub |
| requires_python | >=3.6 |
| license | |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# **B**io**F**ormats **I**nput/**O**utput utility (bfio)
This tool is a simplified but powerful interface to the
[Bioformats java library](https://www.openmicroscopy.org/bio-formats/).
It makes use of Cell Profilers
[python-bioformats](https://github.com/CellProfiler/python-bioformats)
package to access the Bioformats library. One of the issues with using the
`python-bioformats` package is reading and writing large image planes (>2GB).
The challenge lies in the way Bioformats reads and writes large image planes,
using an `int` value to index the file. To get around this, files can be read or
written in chunks and the classes provided in `bfio` handle this automatically.
The `BioWriter` class in this package only writes files in the `.ome.tif`
format, and automatically sets the tile sizes to 1024.
Docker containers with all necessary components are available (see
**Docker Containers** section).
## Documentation
Documentation is available on
[Read the Docs](https://bfio.readthedocs.io/en/latest/).
## Universal Container Components
All containers contain the follow components:
1. Python 3.8
2. [numpy](https://pypi.org/project/numpy/1.19.1/) (1.19.1)
3. [imagecodecs](https://pypi.org/project/imagecodecs/2020.5.30/) (2020.5.30, built with `--lite` option)
4. [tifffile](https://pypi.org/project/tifffile/2020.7.4/) (2020.7.4)
5. bfio (version 2.0.5)
Containers ending with `-java` also contain:
6. openjdk-8
7. [python-javabridge](https://pypi.org/project/python-javabridge/4.0.0/) (version 4.0.0)
8. [python-bioformats](https://pypi.org/project/python-bioformats/4.0.0/) (version 4.0.0)
9. [loci-tools.jar](https://downloads.openmicroscopy.org/bio-formats/6.1.0/artifacts/) (Version 6.1.0)
## Docker Containers
All containers can use the Python backend, but only the containers with Java may
use the Java backend.
### ~labshare/polus-bfio-util:2.0.5~
The alpine container for `bfio` is currently unavailable.
~*Additional Python container tags:* `2.0.5-alpine`, `2.0.5-python`,~
~`2.0.5-alpine-python`~
~*Containers with Java:* `2.0.5-java`, `2.0.5-alpine-java`~
~This container is built on Alpine Linux. This is the smallest bfio container,~
~but also the most difficult to install additional requirements on. The Python~
~containers (98MB) are much smaller than the Java containers (383MB).~
### labshare/polus-bfio-util:2.0.5-slim-buster
*Additional Python container tags:* `2.0.5-slim-buster-python`
*Containers with Java:* `2.0.5-slim-buster-java`
This container is built on a stripped down version of Debian Buster. This
container is larger than the `alpine` version, but easier to install new Python
packages on since `manylinux` wheels can be installed on it. However, if a
package requires compilation, a compiler will need to be installed.
### labshare/polus-bfio-util:2.0.5-tensorflow
*Additional Python container tags:* `2.0.5-tensorflow-python`
*Containers with Java:* No Java containers
This container is built on Debian Buster and includes Tensorflow 2.1.0 and all
necessary GPU drivers to run Tensorflow on an NVIDIA graphics card.
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"description": "# **B**io**F**ormats **I**nput/**O**utput utility (bfio)\n\nThis tool is a simplified but powerful interface to the\n[Bioformats java library](https://www.openmicroscopy.org/bio-formats/).\nIt makes use of Cell Profilers\n[python-bioformats](https://github.com/CellProfiler/python-bioformats)\npackage to access the Bioformats library. One of the issues with using the\n`python-bioformats` package is reading and writing large image planes (>2GB).\nThe challenge lies in the way Bioformats reads and writes large image planes,\nusing an `int` value to index the file. To get around this, files can be read or\nwritten in chunks and the classes provided in `bfio` handle this automatically.\nThe `BioWriter` class in this package only writes files in the `.ome.tif`\nformat, and automatically sets the tile sizes to 1024.\n\nDocker containers with all necessary components are available (see\n**Docker Containers** section).\n\n## Documentation\n\nDocumentation is available on\n[Read the Docs](https://bfio.readthedocs.io/en/latest/).\n\n## Universal Container Components\n\nAll containers contain the follow components:\n\n1. Python 3.8\n2. [numpy](https://pypi.org/project/numpy/1.19.1/) (1.19.1)\n3. [imagecodecs](https://pypi.org/project/imagecodecs/2020.5.30/) (2020.5.30, built with `--lite` option)\n4. [tifffile](https://pypi.org/project/tifffile/2020.7.4/) (2020.7.4)\n5. bfio (version 2.0.5)\n\nContainers ending with `-java` also contain:\n\n6. openjdk-8\n7. [python-javabridge](https://pypi.org/project/python-javabridge/4.0.0/) (version 4.0.0)\n8. [python-bioformats](https://pypi.org/project/python-bioformats/4.0.0/) (version 4.0.0)\n9. [loci-tools.jar](https://downloads.openmicroscopy.org/bio-formats/6.1.0/artifacts/) (Version 6.1.0)\n\n## Docker Containers\n\nAll containers can use the Python backend, but only the containers with Java may\nuse the Java backend. \n\n### ~labshare/polus-bfio-util:2.0.5~\n\nThe alpine container for `bfio` is currently unavailable.\n\n~*Additional Python container tags:* `2.0.5-alpine`, `2.0.5-python`,~\n~`2.0.5-alpine-python`~\n\n~*Containers with Java:* `2.0.5-java`, `2.0.5-alpine-java`~\n\n~This container is built on Alpine Linux. This is the smallest bfio container,~\n~but also the most difficult to install additional requirements on. The Python~\n~containers (98MB) are much smaller than the Java containers (383MB).~\n\n### labshare/polus-bfio-util:2.0.5-slim-buster\n\n*Additional Python container tags:* `2.0.5-slim-buster-python`\n\n*Containers with Java:* `2.0.5-slim-buster-java`\n\nThis container is built on a stripped down version of Debian Buster. This\ncontainer is larger than the `alpine` version, but easier to install new Python\npackages on since `manylinux` wheels can be installed on it. However, if a\npackage requires compilation, a compiler will need to be installed.\n\n### labshare/polus-bfio-util:2.0.5-tensorflow\n\n*Additional Python container tags:* `2.0.5-tensorflow-python`\n\n*Containers with Java:* No Java containers\n\nThis container is built on Debian Buster and includes Tensorflow 2.1.0 and all\nnecessary GPU drivers to run Tensorflow on an NVIDIA graphics card.\n\n",
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