Tako is a image processing workflow engine for high-performance computing
Tako reduces the complexity of high-performance image processing by abstracting the software-stack and the data-management layer, allowing complex workflows to happen with very little effort involved. This is possible by having a workflow engine and a common data format between stages, a stage output can be a stage input.
i.e. A workflow that requires the sequence image alignment>correction>segmentation>visualization can be written
in tako like this:
examples/big_workflow.py
#!python
# Import tako.arms
from tako.arms.alignment import Alignment
from tako.arms.correction import Correction
from tako.arms.segmentation import Segmentation
from tako.arms.visualization import Visualization
from tako.head import head
- Define each stage with a dictionary
setup
#!python
# Alignment block
alignment = Alignment(setup={"algorithm": "sift",
"data": "examples/data/data.raw",
"params": {"fnum": 10,
"sigma": 0.001}})
#!python
# Correction block
correction = Correction(setup = {setup={"algorithm": "drift-correction",
"data": alignment.output(),
"params": {"elastic": -0.2})
#!python
# Segmentation block
segmentation = Segmentation(setup = {"algorithm": "mean-shift",
"data": correction.output(),
"params": {"sigma": 0.1,
"epsilon": 0.01}})
#!python
# Visualization block
visualization = Visualization(setup = {"algorithm": "3d-render",
"data": segmentation.output(),
"params": {"res": 100})
#!python
# Execution block
head.do_workflow.inputs(inputs=[alignment, correction, segmentation, visualization])
Tako also allows you to integrate ImageJ macros and plugins into your workflows.
i.e. Edge detection using ImageJ's run("Find Edges"); method.
examples/imagej_macro.py
#!python
from tako.arms.correction import Correction
from tako.head import head
correction = Correction(setup={"algorithm": "ijmacro",
"data": "examples/data/Lenna.png",
"params": {'macro': "tako/bin/correction/imagej-macro.ijm"}
})
do = head.do_workflow(setup=[correction])
bin/correction/imagej-macro_template.ijm
#!java
args = getArgument;
args = split(args,":");
img=args[0];
output=args[1];
setBatchMode(true);
open(img);
// START ImageJ macro
run("Find Edges");
// END ImageJ macro
saveAs("Tiff", output);
close();
タコ (Tako) has two main components, tako.arms where the workflows are templated, and tako.head where the workflow engine [[Tigres]] manages arm assignments.
- Joaquin Correa
- Tigres team