A Weakly Supervised Method for Instance Segmentation of Biological Cells

We present a weakly supervised deep learning method to perform instance segmentation of cells present in microscopy images. Annotation of biomedical images in the lab can be scarce, incomplete, and inaccurate. This is of concern when supervised learning is used for image analysis as the discriminative power of a learning model might be compromised in these situations. To overcome the curse of poor labeling, our method focuses on three aspects to improve learning: i) we propose a loss function operating in three classes to facilitate separating adjacent cells and to drive the optimizer to properly classify underrepresented regions; ii) a contour-aware weight map model is introduced to strengthen contour detection while improving the network generalization capacity; and iii) we augment data by carefully modulating local intensities on edges shared by adjoining regions and to account for possibly weak signals on these edges. Generated probability maps are segmented using different methods, with the watershed based one generally offering the best solutions, specially in those regions where the prevalence of a single class is not clear. The combination of these contributions allows segmenting individual cells on challenging images. We demonstrate our methods in sparse and crowded cell images, showing improvements in the learning process for a fixed network architecture.

Fast and Robust Multiple ColorChecker Detection using Deep Convolutional Neural Networks

ColorCheckers are reference standards that professional photographers and filmmakers use to ensure predictable results under every lighting condition. The objective of this work is to propose a new fast and robust method for automatic ColorChecker detection. The process is divided into two steps: (1) ColorCheckers localization and (2) ColorChecker patches recognition. For the ColorChecker localization, we trained a detection convolutional neural network using synthetic images. The synthetic images are created with the 3D models of the ColorChecker and different background images. The output of the neural networks are the bounding box of each possible ColorChecker candidates in the input image. Each bounding box defines a cropped image which is evaluated by a recognition system, and each image is canonized with regards to color and dimensions. Subsequently, all possible color patches are extracted and grouped with respect to the center's distance. Each group is evaluated as a candidate for a ColorChecker part, and its position in the scene is estimated. Finally, a cost function is applied to evaluate the accuracy of the estimation. The method is tested using real and synthetic images. The proposed method is fast, robust to overlaps and invariant to affine projections. The algorithm also performs well in case of multiple ColorCheckers detection.