Napari plugin for iteratively improving 3D instance segmentation of cells (u-net x watershed)

Related tags

Image Processing iterseg
Overview

iterseg

License PyPI Python Version tests codecov napari hub

napari plugin for iteratively improving unet-watershed segmentation

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install iterseg via pip:

pip install iterseg

To install latest development version :

pip install git+https://github.com/abigailmcgovern/iterseg.git

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "iterseg" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

You might also like...
A napari plugin for visualising and interacting with electron cryotomograms.
A napari plugin for visualising and interacting with electron cryotomograms.

napari-tomoslice A napari plugin for visualising and interacting with electron cryotomograms. Installation You can install napari-tomoslice via pip: p

null 3 Jan 3, 2023
A napari plugin for visualising and interacting with electron cryotomograms
A napari plugin for visualising and interacting with electron cryotomograms

napari-subboxer A napari plugin for visualising and interacting with electron cryotomograms. Installation You can install napari-subboxer via pip: pip

null 3 Nov 25, 2021
A napari plugin to inspect data within a cisTEM project

napari-cistem A plugin to inspect data within a cisTEM project This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-na

Johannes Elferich 1 Nov 7, 2021
A meta plugin for processing timelapse data timepoint by timepoint in napari
A meta plugin for processing timelapse data timepoint by timepoint in napari

napari-time-slicer A meta plugin for processing timelapse data timepoint by timepoint. It enables a list of napari plugins to process 2D+t or 3D+t dat

Robert Haase 2 Oct 13, 2022
A simple plugin to view APR images in napari

napari-apr-viewer A simple plugin to view APR images in napari This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-

null 5 Jan 24, 2022
Plugin adapted from Ultralytics to bring YOLOv5 into Napari
Plugin adapted from Ultralytics to bring YOLOv5 into Napari

napari-yolov5 Plugin adapted from Ultralytics to bring YOLOv5 into Napari. Training and detection can be done using the GUI. Training dataset must be

null 2 May 5, 2022
Leveraging Instance-, Image- and Dataset-Level Information for Weakly Supervised Instance Segmentation

Leveraging Instance-, Image- and Dataset-Level Information for Weakly Supervised Instance Segmentation This paper has been accepted and early accessed

Yun Liu 39 Sep 20, 2022
Turn images of tables into CSV data. Detect tables from images and run OCR on the cells.
Turn images of tables into CSV data. Detect tables from images and run OCR on the cells.

Table of Contents Overview Requirements Demo Modules Overview This python package contains modules to help with finding and extracting tabular data fr

Eric Ihli 311 Dec 24, 2022
Learning cell communication from spatial graphs of cells
Learning cell communication from spatial graphs of cells

ncem Features Repository for the manuscript Fischer, D. S., Schaar, A. C. and Theis, F. Learning cell communication from spatial graphs of cells. 2021

Theis Lab 77 Dec 30, 2022
Python package for handwriting and sketching in Jupyter cells
Python package for handwriting and sketching in Jupyter cells

ipysketch A Python package for handwriting and sketching in Jupyter notebooks. Usage A movie is worth a thousand pictures is worth a million words...

Matthias Baer 16 Jan 5, 2023
Official code for On Path Integration of Grid Cells: Group Representation and Isotropic Scaling (NeurIPS 2021)
Official code for On Path Integration of Grid Cells: Group Representation and Isotropic Scaling (NeurIPS 2021)

On Path Integration of Grid Cells: Group Representation and Isotropic Scaling This repo contains the official implementation for the paper On Path Int

Ruiqi Gao 39 Nov 10, 2022
nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order
nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order

nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order

null 150 Jan 7, 2023
Identifies the faulty wafer before it can be used for the fabrication of integrated circuits and, in photovoltaics, to manufacture solar cells.

Identifies the faulty wafer before it can be used for the fabrication of integrated circuits and, in photovoltaics, to manufacture solar cells. The project retrains itself after every prediction, making it more robust and generalized over time.

Arun Singh Babal 2 Jul 1, 2022
Skull shaped MOSFET cells for the Efabless's 130nm process

SkullFET Skull shaped MOSFET cells for the Efabless's 130nm process List of cells Inverter Copyright (C) 2021 Uri Shaked

Wokwi 3 Dec 14, 2022
A two-player strategy game played on a rectangular grid made up of smaller square cells of chocolate 🍫 or cookies 🍪
A two-player strategy game played on a rectangular grid made up of smaller square cells of chocolate 🍫 or cookies 🍪

Chomp Game ©️ Chomp is a two-player strategy game played on a rectangular grid made up of smaller square cells of chocolate 🍫 or cookies 🍪 , which c

Farivar Tabatabaei 2 Feb 2, 2022
U^2-Net - Portrait matting This repository explores possibilities of using the original u^2-net model for portrait matting.
U^2-Net - Portrait matting This repository explores possibilities of using the original u^2-net model for portrait matting.

U^2-Net - Portrait matting This repository explores possibilities of using the original u^2-net model for portrait matting.

Dennis Bappert 104 Nov 25, 2022
The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

MIC-DKFZ 1.2k Jan 4, 2023
Neural networks applied in recognizing guitar chords using python, AutoML.NET with C# and .NET Core
Neural networks applied in recognizing guitar chords using python, AutoML.NET with C# and .NET Core

Chord Recognition Demo application The demo application is written in C# with .NETCore. As of July 9, 2020, the only version available is for windows

Andres Mauricio Rondon Patiño 24 Oct 22, 2022
U-2-Net: U Square Net - Modified for paired image training of style transfer
U-2-Net: U Square Net - Modified for paired image training of style transfer

U2-Net: U Square Net Modified for paired image training of style transfer This is an unofficial repo making use of the code which was made available b

Doron Adler 43 Oct 3, 2022
Owner
Abigail McGovern
PhD Student or 18th Century porcelain cabbage art.
Abigail McGovern
GitHub
A simple plugin to view APR images in napari

napari-apr-viewer A simple plugin to view APR images in napari This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-

null 5 Jan 24, 2022
Sample data for the napari image viewer.

napari-demo-data Sample data for the napari image viewer. This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugi

Genevieve Buckley 1 Nov 8, 2021
A suite of useful tools based on 3D interactivity in napari

napari-threedee A suite of useful tools based on 3D interactivity in napari This napari plugin was generated with Cookiecutter using @napari's cookiec

null 11 Dec 14, 2022
Napari simpleitk image processing

napari-simpleitk-image-processing (n-SimpleITK) Process images using SimpleITK in napari Usage Filters of this napari plugin can be found in the Tools

Robert Haase 11 Dec 19, 2022
A simple image-level annotation tool supporting multi-channel images for napari.

napari-labelimg4classification A simple image-level annotation tool supporting multi-channel images for napari. This napari plugin was generated with

null 4 May 16, 2022
Napari 3D Ortho Viewer - an ortho viewer for napari for 3D images

napari-3d-ortho-viewer Napari 3D Ortho Viewer - an ortho viewer for napari for 3D images This napari plugin was generated with Cookiecutter using @nap

niklas netter 5 Nov 28, 2022
Python for .NET is a package that gives Python programmers nearly seamless integration with the .NET Common Language Runtime (CLR) and provides a powerful application scripting tool for .NET developers.

pythonnet - Python.NET Python.NET is a package that gives Python programmers nearly seamless integration with the .NET Common Language Runtime (CLR) a

null 3.5k Jan 6, 2023
PyNHD is a part of HyRiver software stack that is designed to aid in watershed analysis through web services.

A part of HyRiver software stack that provides access to NHD+ V2 data through NLDI and WaterData web services

Taher Chegini 23 Dec 14, 2022
This is the code repository for LRM Stochastic watershed model.

LRM-Squannacook Input data for generating stochastic streamflows are observed and simulated timeseries of streamflow. their format needs to be CSV wit

null 1 Feb 14, 2022
Napari plugin for loading Bitplane Imaris files .ims

napari-imaris-loader Napari plugin for loading Bitplane Imaris files '.ims'. Notes: For this plugin to work "File/Preferences/Experimental/Render Imag

Alan Watson 4 Dec 1, 2022