Automatic segmentation of electron microscopy volumes
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README.md

gala: segmentation of nD images Picture

Gala is a Python library for performing and evaluating image segmentation, distributed under the open-source, BSD-like Janelia Farm license. It implements the algorithm described in Nunez-Iglesias et al., PLOS ONE, 2013.

If you use this library in your research, please cite:

Nunez-Iglesias J, Kennedy R, Plaza SM, Chakraborty A and Katz WT (2014) Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages. Front. Neuroinform. 8:34. doi:10.3389/fninf.2014.00034

If you use or compare to the GALA algorithm in your research, please cite:

Nunez-Iglesias J, Kennedy R, Parag T, Shi J, Chklovskii DB (2013) Machine Learning of Hierarchical Clustering to Segment 2D and 3D Images. PLoS ONE 8(8): e71715. doi:10.1371/journal.pone.0071715

Gala supports n-dimensional images (images, volumes, videos, videos of volumes...) and multiple channels per image. It is compatible with Python 3.5.

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Requirements

After version 0.3, Gala requires Python 3.5 to run. For a full list of dependencies, see the requirements.txt file.

Optional dependencies

In its original incarnation, this project used Vigra for the random forest classifier. Installation is less simple than scikit-learn, which has emerged in recent years as a truly excellent implementation and is now recommended. Tests in the test suite expect scikit-learn rather than Vigra. You can also use any of the scikit-learn classifiers, including their world-class random forest implementation.

Installation

Installing gala

Gala is a Python library with limited Cython extensions and can be installed in three ways:

  • Use pip: pip install gala.
  • Add the gala directory to your PYTHONPATH environment variable, or
  • Use distutils to install it into your preferred python environment:
$ python setup.py install

Installing requirements

Though you can install all the requirements yourself, as most are available in the Python Package Index (PyPI) and can be installed with simple commands, the easiest way to get up and running is to use miniconda. Once you have the conda command, you can create a fully-functional gala environment with conda env create -f environment.yml (inside the gala directory).

Installing with Buildem

Alternatively, you can use Janelia's own buildem system to automatically download, compile, test, and install requirements into a specified buildem prefix directory. (You will need CMake.)

$ cmake -D BUILDEM_DIR=/path/to/platform-specific/build/dir <gala directory>
$ make

You might have to run the above steps twice if this is the first time you are using the buildem system.

On Mac, you might have to install compilers (such as gcc, g++, and gfortran).

Testing

The test coverage is rather small, but it is still a nice way to check you haven't completely screwed up your installation. After installing gala, go to the code directory and type:

$ py.test

You need to have pytest and pytest-cov installed, both of which are available through PyPI.

Usage

An example script, example.py, exists in the tests/example-data directory. We step through it here for a quick rundown of gala's capabilities.

First, import gala's submodules:

from gala import imio, classify, features, agglo, evaluate as ev

Next, read in the training data: a ground truth volume (gt_train), a probability map (pr_train) and a superpixel or watershed map (ws_train).

gt_train, pr_train, ws_train = (map(imio.read_h5_stack,
                                ['train-gt.lzf.h5', 'train-p1.lzf.h5',
                                 'train-ws.lzf.h5']))

A feature manager is a callable object that computes feature vectors from graph edges. The object has the following responsibilities, which it can inherit from classify.base.Null:

  • create a (possibly empty) feature cache on each edge and node, precomputing some of the calculations needed for feature computation;
  • maintain the feature cache throughout node merges during agglomeration; and,
  • compute the feature vector from the feature caches when called with the inputs of a graph and two nodes.

Feature managers can be chained through the features.Composite class.

fm = features.moments.Manager()
fh = features.histogram.Manager()
fc = features.base.Composite(children=[fm, fh])

With the feature manager, and the above data, we can create a region adjacency graph or RAG, and use it to train the agglomeration process:

g_train = agglo.Rag(ws_train, pr_train, feature_manager=fc)
(X, y, w, merges) = g_train.learn_agglomerate(gt_train, fc)[0]
y = y[:, 0] # gala has 3 truth labeling schemes, pick the first one

X and y above have the now-standard scikit-learn supervised dataset format. This means we can use any classifier that satisfies the scikit-learn API. Below, we use a simple wrapper around the scikit-learn RandomForestClassifier.

rf = classify.DefaultRandomForest().fit(X, y)

The composition of a feature map and a classifier defines a policy or merge priority function, which will determine the agglomeration of a volume of hereby unseen data (the test volume).

learned_policy = agglo.classifier_probability(fc, rf)

pr_test, ws_test = (map(imio.read_h5_stack,
                        ['test-p1.lzf.h5', 'test-ws.lzf.h5']))
g_test = agglo.Rag(ws_test, pr_test, learned_policy, feature_manager=fc)

The best expected segmentation is obtained at a threshold of 0.5, when a merge has even odds of being correct or incorrect, according to the trained classifier.

g_test.agglomerate(0.5)

The RAG is a model for the segmentation. To extract the segmentation itself, use the get_segmentation function. This is a map of labels of the same shape as the original image.

seg_test1 = g_test.get_segmentation()

Gala transparently supports multi-channel probability maps. In the case of EM images, for example, one channel may be the probability that a given pixel is part of a cell boundary, while the next channel may be the probability that it is part of a mitochondrion. The feature managers work identically with single and multi-channel features.

# p4_train and p4_test have 4 channels
p4_train = imio.read_h5_stack('train-p4.lzf.h5')
# the existing feature manager works transparently with multiple channels!
g_train4 = agglo.Rag(ws_train, p4_train, feature_manager=fc)
(X4, y4, w4, merges4) = g_train4.learn_agglomerate(gt_train, fc)[0]
y4 = y4[:, 0]
rf4 = classify.DefaultRandomForest().fit(X4, y4)
learned_policy4 = agglo.classifier_probability(fc, rf4)
p4_test = imio.read_h5_stack('test-p4.lzf.h5')
g_test4 = agglo.Rag(ws_test, p4_test, learned_policy4, feature_manager=fc)
g_test4.agglomerate(0.5)
seg_test4 = g_test4.get_segmentation()

For comparison, gala allows the implementation of many agglomerative algorithms, including mean agglomeration (below) and LASH.

g_testm = agglo.Rag(ws_test, pr_test,
                    merge_priority_function=agglo.boundary_mean)
g_testm.agglomerate(0.5)
seg_testm = g_testm.get_segmentation()

Evaluation

The gala library contains numerous evaluation functions, including edit distance, Rand index and adjusted Rand index, and our personal favorite, the variation of information (VI):

gt_test = imio.read_h5_stack('test-gt.lzf.h5')
import numpy as np
results = np.vstack((
    ev.split_vi(ws_test, gt_test),
    ev.split_vi(seg_testm, gt_test),
    ev.split_vi(seg_test1, gt_test),
    ev.split_vi(seg_test4, gt_test)
    ))
print(results)

This should print something like:

[[ 0.1845286   1.64774412]
 [ 0.18719817  1.16091003]
 [ 0.38978567  0.28277887]
 [ 0.39504714  0.2341758 ]]

Each row is an evaluation, with the first number representing the undersegmentation error or false merges, and the second representing the oversegmentation error or false splits, both measured in bits.

(Results may vary since there is some randomness involved in training a random forest, and the datasets are small.)

As mentioned earlier, many other evaluation functions are available. See the documentation for the evaluate package for more information.

# rand index and adjusted rand index
ri = ev.rand_index(seg_test1, gt_test)
ari = ev.adj_rand_index(seg_test1, gt_test)
# Fowlkes-Mallows index
fm = ev.fm_index(seg_test1, gt_test)

Other options

Gala supports a wide array of merge priority functions to explore your data. We can specify the median boundary probability with the merge_priority_function argument to the RAG constructor:

g_testM = agglo.Rag(ws_test, pr_test,
                    merge_priority_function=agglo.boundary_median)

A user can specify their own merge priority function. A valid merge priority function is a callable Python object that takes as input a graph and two nodes, and returns a real number.

To be continued...

That's a quick summary of the capabilities of Gala. There are of course many options under the hood, many of which are undocumented... Feel free to push me to update the documentation of your favorite function!