Deep End-to-end Fingerprint Denoising and Inpainting
Abstract This work describes our winning solution for the Chalearn LAP Inpainting
Competition Track 3 – Fingerprint Denoising and In-painting. The objective
of this competition is to reduce noise, remove the background pattern and replace
missing parts of fingerprint images in order to simplify the verification made by humans
or third-party software. In this paper, we use a U-Net like CNN model that
performs all those steps end-to-end after being trained on the competition data in
a fully supervised way. This architecture and training procedure achieved the best
results on all three metrics of the competition .
Fingerprints play an important role in privacy and identity verification but can also
be used in forensic operations. This means that having the ability to accurately pro-
cess and match fingerprints can be a valuable asset. This is what motivates this work
where the objective is to retrieve a cleaned image of a fingerprint out of a noisy, dis-
Generally, images contain noise and perturbations that may be due to the acquisition
device, compression method or post-processing done. This motivates the research
on tools and methods like denoising and inpainting to alleviate this problem. They
are used as a pre-processing step in order to simplify the subsequent tasks and im-
prove the target performance. In our case, the end goal is to improve the fingerprint
false acceptance rate or the false rejection rate.
One approach to denoising is the TV method  which is based on the principle
that noisy images have a high total variation, the aim of the TV approach is to thus
reduce the regularized total variation of the input image.
 reviews multiples methods to denoising like the Gaussian smoothing model or
translation invariant wavelet thresholding, among others.
A more recent direction to denoising and inpainting is based on deep neural net-
works where a sequence of convolution layers are optimized to learn a mapping
from a noisy image to a ”clean” version of that image.  studies the same problem
as the Chalearn competition and uses and proposes encoder-decoder architecture to
solve it.  shows that using skip connections helps avoid the issues related to train-
ing deep neural networks like the vanishing gradient problem.
Similar to ,  introduces an architecture called U-net that is also an encoder-
decoder type with skip connections that is used primarily for image segmentation.
U-Net showed impressive results when used along with data augmentation even
when the size of the dataset is small. In this work, we are going to use an archi-
tecture that is similar to U-Net and show that it can be applied successfully even
outside pure segmentation tasks.
The dataset provided by the organizers consisted of 84000 (200, 400) fingerprint im-
ages generated using Anguli: Synthetic Fingerprint Generator. Those images were
then artificially degraded by adding a background and random transformations (blur,
brightness, contrast, elastic transformation, occlusion, scratch, resolution, rotation).
The objective is to retrieve the clean fingerprint image from the degraded version.
We use the set of parallel data (Degraded image, Clean image) as the (Input, Ground
Truth) of our model training.
3 Proposed solution
The architecture used is described in Figure 1 and is similar to the one introduced
in , except that we pad the input with zeros instead of mirroring the edges. The
major advantage of this architecture is its ability to take into account a wider context
when making a prediction for a pixel. This is thanks to the large number of channels
used in the up-sampling operation.
3.2 Image processing
Input image processing : We apply this sequence of processing steps before feeding
it to the CNN.
Deep End-to-end Fingerprint Denoising and Inpainting
- Normalization : we divide pixel intensities by 255 so they are in the 0-1 range.
- Re-sizing : The network expects each dimension of the input image to be divisible by 24 because of the pooling operations.
- Data augmentation : Random flip (Horizontal or vertical or both), Random Shear, Random translation (Horizontal or vertical or both), Random Zoom, Random Contrast change, Random Saturation change, Random Rotation. Performed during training only.
Output image processing : We apply this sequence of processing steps before sub-
mitting the results.
- Re-sizing : We re-size the size of the output to the original size of the input.
- Min-Max scaling : We min-max scale the output to the 0-255 range.
3.3 Training Procedure
We use Adam optimizer with an initial learning rate of 1e −4
that is reduced by afactor of 0.5 each time the validation loss plateaued for more than 3
epochs and the learning is stopped if the validation loss does not improve for the last 5 epochs.
Implementation was done using Keras  with Tensorflow backend on a 1070 GTX card.
Table 1: Best Test results in bold
Our approach gets the best results on all three metrics. Even though we only used
the MAE in our loss function, it seems to have acted a good proxy for the other two
As a comparison rgsl888 used a similar architecture to ours but added dilated con-
volutions to expand the receptive field of the network. hcilab used a hierarchical
approach and sukeshadigav used an M-Net Based Convolutional Neural Network.
5 Advantages and Limitations
Our approach has the merit of being end-to-end, requires minimal pre-processing to
the input and uses a single model. All of this simplifies the use of the approach in a
This approach also comes with few limitations like the fact that the train and test
sets are both synthetic, which means that we do not know if the same performance
will be preserved if the trained model is applied to real data. Another issue is that
since the model is trained in a fully supervised way, then it is unlikely to generalize
beyond the perturbations that it was trained on. This reaffirms the need to train on
real fingerprint data.
6 Conclusion and future work
In this paper, we describe the approach we used to achieve 1st place on the Chalearn
LAP In-painting Competition Track 3 – Fingerprint Denoising and In-painting. We
describe the pre-processing steps needed, data augmentation, training procedure and
network architecture used.
In our future work, we will experiment with transferring representations from higher
level supervised tasks or by using a semi-supervised approach like adding an adver-
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