Release notes - August 9, 2021

Recently published apps

SBG Image Processing Toolkit 

SBG Image Processing Toolkit consists of apps that enable various stages of machine learning image processing. Seamless integration between the tools of this toolkit provides an easy and logical analysis flow, while enabling support of various data types, preprocessing steps and utilizing computation capabilities of BioData Catalyst powered by Seven Bridges.

1. SBG Deep Learning Image Classification Exploratory Workflow is an image classifier pipeline that relies on the transfer learning approach. This allows the use of pre-trained models as the starting point for building a model adjusted to given image datasets. Furthermore, the pipeline allows training of the model for a variety of hyperparameter combinations in parallel by utilizing multiple GPU instances, while detailed metrics and visualizations help determine the best configuration that can later be used to make predictions on new data instances.
2. SBG Deep Learning Prediction is an image classifier tool that classifies unlabeled images based on labeled data. It is intended as a final step after the SBG Deep Learning Image Classification Exploratory Workflow. Testing different configurations in parallel with the exploratory workflow and finding the best model configuration for the given dataset, then using SBG Deep Learning Prediction with that configuration and all available labeled images as the training data provides the optimal training conditions which lead to the best classification results.
3. SBG Histology Whole Slide Image Preprocessing takes SVS histopathology images, removes various artifacts, and outputs the desired number of best quality tiles in PNG format that consist of at least 90% tissue.
4. SBG X-Ray Image Preprocessing Workflow performs the selected X-ray image enhancement algorithm: unsharp masking (UM), high-frequency emphasis filtering (HEF) or contrast limited adaptive histogram equalization (CLAHE).
5. SBG Stain Normalization involves casting an array of images in the stain colors of a target image. Stain normalization is used as a histopathology image preprocessing step to reduce the color and intensity variations present in stained images obtained from different laboratories.
6. SBG Medical Image Convert performs medical image format conversion. If the input data are medical images in a non-standard format (e.g. SVS, TIFF, DCM or DICOM), SBG Medical Image Convert converts them to PNG format.
7. SBG Split Folders organizes an image directory into the train and test subdirectory structure. These directories are necessary inputs for SBG Deep Learning Image Classification Exploratory Workflow and SBG Deep Learning Prediction.

HistoQC

HistoQC is an open-source quality control tool for digital pathology slides. It performs fast quality control to not only identify and delineate artefacts but also discover cohort-level outliers (e.g., slides stained darker or lighter than others in the cohort). It outputs an interactive user interface for easy viewing and understanding of the results.

Minimac4

Minimac4 is a genetic imputation algorithm that can be used to impute genotypes in a genomic region starting from a reference panel in M3VCF format and pre-phased target GWAS haplotypes.

BOLT-LMM

BOLT-LMM is a tool that tests the association between genotypes and phenotypes using a linear mixed model.