This python toolbox performs registration between 2-D microscopy images from the same tissue section or serial sections in several ways to achieve imaging mass spectrometry (IMS) experimental goals.
This code supports the following works and enables others to perform the workflows outlined in the following works, please cite them if you use this toolbox:
Advanced Registration and Analysis of MALDI Imaging Mass Spectrometry Measurements through Autofluorescence Microscopy, 10.1021/acs.analchem.8b02884
Next Generation Histology-directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy, 10.1021/acs.analchem.8b02885
This is an implementation of Mask R-CNN on Python 3, Keras, and TensorFlow. The model generates bounding boxes and segmentation masks for each instance of an object in the image. It's based on Feature Pyramid Network (FPN) and a ResNet101 backbone.
NEUBIAS-WG5 workflow for nuclei segmentation using Mask-RCNN. The workflow uses Matterport Mask-RCNN. Keras implementation. The model was trained with Kaggle 2018 Data Science Bowl images.
