Just wanted to take a moment and share some quick stain normalization type experimental results. We have a trained in-house nuclei segmentation model which works fairly well when the test images have similar stain presentation properties, but when new datasets arrive which are notably different we tend to see a decreased classifier performance.
Here we look at one of these images and ways of improving classifier robustness.
Continue reading On Stain Normalization in Deep Learning
One of the common ways of increasing the size of a training set is to augment the original data with a set of modified patches. These modifications often include (a) rotations, (b) mirroring, (c) lighting adjustment, (d) affine transformations (sheering, etc), (e) magnification modification, (f) addition of noise, etc. This blog post discusses how to do the most trivial modification, rotation, in real-time using a python layer through Nvidia Digits. Given this code, it should be easy to add on other desired augmentations.
Continue reading Real time Data Augmentation using Nvidia Digits + Python Layer
Our publication “Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases” , showed how to use deep learning to address many common digital pathology tasks. Since then, many improvements have been made both in the field and in my implementation of them. In this blog post, I re-address the nuclei segmentation use case using the latest and greatest approaches.
Continue reading Revised Deep Learning approach using Matlab + Caffe + Python
One of the challenges in working in digital pathology is that the associated images can be excessively large, too large to load fully into memory, as well as too large to use in common pipelines. For example, a Aperio SVS file that we’ll look at today is 60,000 x 42,600 pixels. If we tried to load such an image, in RGB space, uncompressed it would require ~7GB, making it too large to consider using in our deep learning pipelines as there wouldn’t be enough RAM on the GPU for both the data and the filter activations.
Continue reading Dividing and re-merging large images (Humpty Dumpty)
This blog post is based on the net surgery example provided by Caffe. It takes the concept and expands it to a working example to produce pixel-wise output images, generating output in ~2 seconds (simple approach) or ~35 seconds (advanced approach) for a 2,000 x 2,000 image, an improvement from the ~15 hours of a naive pixel wise approach.
Continue reading Efficient pixel-wise deep learning on large images
Here we discuss how to install Nvidia Digits. This is mostly intended as a documentation of the process I had to go through to install it in my lab environment on a single stand-alone machine housing 3 gpus.
Continue reading How to Install Nvidia Digits
This blog posts explains how to train a deep learning lymphoma sub-type classifier in accordance with our paper “Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases”.
Continue reading Use Case 7: Lymphoma Sub-Type Classification
This blog posts explains how to train a deep learning mitosis detector in accordance with our paper “Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases”.
Continue reading Use Case 5: Mitosis Detection
This blog posts explains how to train a deep learning Invasive Ductal Carcinoma (IDC) classifier in accordance with our paper “Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases”.
Continue reading Use Case 6: Invasive Ductal Carcinoma (IDC) Segmentation