YAPiC is developed by the Image and Data Analysis Facility, Core Reseach Facilities of the DZNE (German Center for Neurodegenerative Diseases). CLI Documentation CLI Documentation
What is YAPiC for?
With YAPiC you can make your own customzied filter (we call it model or classifier) to enhance a certain structure of your choice.
We can, e.g train a model for detection of oak leafs in color images, and use this oak leaf model to filter out all image regions that are not covered by oak leaves:
- Pixels that belong to other leaf types or to no leafs at all are mostly suppressed, they appear dark in the output image.
- Pixels that belong to oak leafs are enhanced, they appear bright in the output image.
The output image is also called a pobability map, because the intensity of each pixel corresponds to the probability of the pixel belonging to an oak leave region.
You can train a model for almost any structure you are interested in, for example to detect a certain cell type ist histological micrographs (here: purkinje cells of the human brain):
Histology data provided by Oliver Kaut (University Clinic Bonn, Dept. of Neurology)
We have used YAPiC for analyzing various microscopy image data. Our experiments are mainly related to neurobiology, cell biology, histopathology and drug discovery (high content screening). However, YAPiC is a very generally applicable tool and can be applied to very different domains. It could be used for detecting e.g. forest regions in satellite images, clouds in landscape photographs or fried eggs in food photography.
- Live cell imaging: Detection of neurites in label-free time lapse imaging.
- Digital Pathology: Detection of specific cell types in histological micrographs.
- Electron Microscopy: Detection of actin filaments in transmission electron micrographs.
Pixel classification in YAPiC is based on deep learning with fully convolutional neural networks. Development of YAPiC started in 2015, when Ronneberger et al. presented a U-shaped fully convolutional neural network that was capable of solving highly challenging pixel classification tasks in bio images, such as tumor classification in histological slides or cell segmentation in brightfield DIC images.
YAPiC was designed to make this new kind of AI powered pixel classification simply applicable, i.e feasible to use for a PhD student in his/her imaging project.
Simply applicable means here in detail:
- Easy to install.
- Working out of the box with 3D multichannel images saved with Fiji.
- Easy collection of label data by utilizing the great Ilastik user interface.
- Support of sparse labels. From our experience, labels can be collected within a few hours by one single person.
- Simple command line and programming interface (Python).
How to use it
Command line interface
yapic train unet_2d "path/to/my/images/*.tif" path/to/my/labels.ilp
yapic predict my_trained_model.h5 path/to/results/
Get hands on YAPiC with the tutorial.
Go to CLI Documentation for more details.
from yapic.session import Session img_path = 'path/to/my/images/*.tif' label_path = 'path/to/my/labels.ilp' model_size_zxy = (5, 572, 572) t = Session() t.load_training_data(img_path, label_path) t.make_model('unet_multi_z', model_size_zxy) t.define_validation_data(0.2) # 80% training data, 20% validation data t.train(max_epochs=5000, steps_per_epoch=48, log_filename='log.csv') t.model.save('my_model.h5')
from yapic.session import Session img_path = 'path/to/my/images/*.tif' results_path = 'path/to/my/results/' t = Session() t.load_prediction_data(img_path, results_path) t.load_model('my_model.h5') t.predict() # applies the classfier to all images in img_path
Try it out with the leaves example dataset
How to install
Install Python 3.6.
- Install Tensorflow
- if you want to use GPU processing (recommended)
pip install tensorflow-gpu==1.8.0
- For CPU processing (just for testing, do not use it in production)
pip install tensorflow
- Install YAPiC
pip install yapic
Windows and Mac
YAPiC is currently only supported on Linux. It runs in principle on Mac OS, but installing Tensorflow with GPU support in currently not that straightforward on Mac OS. We may release Docker images in the future to run YAPiC easily in Windows and Mac workstations.
YAPiC is designed to run on dedicated hardware. In production, it should not run on your everyday-work notebook, but on a dedicated workstation or a server. The reason is, that training a model requires long time (multiple hours to multiple days) and a lot of computing power. Running these processes in the background on your notebook while e.g. writing E-Mails is not feasible. Moreover, you will need powerful GPU hardware that is normally not available on office notebooks.
- Using fast SSD hard drives (PCIe SSDs) for storing training data may increase training speed, compared to conventional hard drives. Have a look at the GPU requirements for Tensorflow
- From our expericence you can have already quite good performance with NVIDIA Geforce boards (mainly intended for gaming). These are cheaper than professional NVIDIA Tesla GPUs.
GPU RAM requirements: RAM of your GPU hardware is often a bottleneck and depends the specific project. RAM requirements depend on the number of classes you want to train and if you use a 2D network or 3D network. Some recommendations, based on our personal experience:
- For training a unet_2D with two classes (foreground, background), 5 GB RAM on your GPU is sufficient.
- For training a unet_multi_z with five z-layers and two classes, 11 GB RAM on GPU is sufficient.