Simple reading and writing classes for tiled tiffs using Bioformats.
Project description
BioFormats Input/Output utility (bfio)
This tool is a simplified but powerful interface to the Bioformats java library. It makes use of Cell Profilers 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 do 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).
Examples
Read an Image
import javabridge
from bfio import BioReader,BioWriter,JARS
from pathlib import Path
# Import javabridge and start the vm
javabridge.start_vm(class_path=JARS)
# Path to bioformats supported image
image_path = Path('path/to/file.ome.tif')
# Create the BioReader object
bf = BioReader(str(image_path))
# Load the full image
image = bf.read_image()
# Only load the first 256x256 pixels, will still load all Z,C,T dimensions
# Note: Images are always 5-dimensional
image = bf.read_image(X=(0,256),Y=(0,256))
# Only load the second channel
image = bf.read_image(C=[1])
# Done executing program, so kill the vm. If the program needs to be run
# again, a new interpreter will need to be spawned to start the vm.
javabridge.kill_vm()
Write an Image
import javabridge
from bfio import BioReader,BioWriter,JARS
from pathlib import Path
# Import javabridge and start the vm
javabridge.start_vm(class_path=JARS)
# Path to bioformats supported image
image_path = Path('path/to/file.ome.tif')
# Create the BioReader object
br = BioReader(str(image_path))
# Load the full image
image = br.read_image()
# Create an image write object, rename the channels
bw = BioWriter(str(image_path.with_name("New_" + image_path.name)),image=image)
bw.channel_names(["Empty","ZO1","Empty"])
bw.write_image(image)
bw.close_image()
# Only save one channel
bw = BioWriter(str(image_path.with_name("New_" + image_path.name)),image=image)
bw.num_c(1)
bw.write_image(image[:,:,0,1,0].reshape((image.shape[0],image.shape[1],1,1,1)))
bw.close_image()
# List the channel names
print(bw.channel_names())
# Done executing program, so kill the vm. If the program needs to be run
# again, a new interpreter will need to be spawned to start the vm.
jutil.kill_vm()
Documentation
Documentation is available on Read the Docs.
Universal Container Components
All containers contain the follow components:
- Python 3.8
- numpy (1.19.1)
- imagecodecs (2020.5.30, built with
--lite
option) - tifffile (2020.7.4)
- bfio (version 2.0.0)
Containers ending with -java
also contain:
- openjdk-8
- python-javabridge (version 4.0.0)
- python-bioformats (version 4.0.0)
- loci-tools.jar (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:2.0.0
Additional Python container tags: 2.0.0-alpine
, 2.0.0-python
,
2.0.0-alpine-python
Containers with Java: 2.0.0-java
, 2.0.0-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:2.0.0-slim-buster
Additional Python container tags: 2.0.0-slim-buster-python
Containers with Java: 2.0.0-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:2.0.0-tensorflow
Additional Python container tags: 2.0.0-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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