Automated workflow for performing multiview reconstruction of large multiview, multichannel, multiillumination time-lapse SPIM data on a high performance computing (HPC) cluster or on a single workstation.
Code to segment yeast cells using a pre-trained mask-rcnn model. We've tested this with yeast cells imaged in fluorescent images and brightfield images, and gotten good results with both modalities. This code implements an user-friendly script that hides all of the messy implementation details and parameters. Simply put all of your images to be segmented into the same directory, and then plug and go.
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.
