Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
How about GridofImagesTranslator?
Reminders:
TF Implementation of Multiple Instance Learning FCN.
We should remove some fat and also host images/binaries/models somewhere else (OSF, mirrors, etc.)
Open Source Cross-Platform C++ library to read CZI image files
Manual, source-code and binaries for the NanoJ-Fluidics project
Maybe, we can add a linting rule which checks that all functions in the api file have docstrings? At least, importNmlAsString is missing a docstring.
Code for my master's thesis. Instance segmentation of fluorescence microscopy images with deep learning.
It would be great to add Doxygen or similar for auto-generation of documentation and start a push towards standardisation of the style and comment/description data as to work with such a system.
Currently the focus of the navcam is hard coded. If you're lucky, the focus is correct, but in most of the time you're not lucky.
So instead of using a hard coded position, we should either:
Experimental tech-demo for PhD thesis in Scientific Markdown; official:
An interactive image processing program for biologists written in Python.
Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools.
:microscope::cocktail: Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ
Java (ImageJ/Fiji) software package for 3D deconvolution microscopy
A scientific publication, describing a way to improve microscopy. This repository hosts everything you need to reproduce our results. Read the publication here: https://andrewgyork.github.io/remote_refocus/
A convex 3D deconvolution algorithm for low photon count fluorescence imaging
A scientific publication, describing a way to improve microscopy. This repository hosts everything you need to reproduce our results. Read the publication here: https://amsikking.github.io/remote_refocus/
Fast and Accurate 3D PSF Computation for Fluorescence Microscopy
Microscope control and image acquisition integrated with ImageJ.
Lattice light-sheet post-processing utility.
rapidSTORM open-source localization microscopy software
Fast and Accurate 3D PSF Computation for Fluorescence Microscopy
Python samples for Micro-Manager: image acquisition and microscope control system
Simple demo of structured illumination microscopy image fusion via Richardson-Lucy deconvolution
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Originally reported by: Oliver Clarke (Bitbucket: olibclarke, GitHub: olibclarke)
Hi,
When using relion_preprocess on the command line to extract particles, the behaviour does not seem to match the documentation. Both my micrographs and coordinate files are located in the directory