This is an implementation of NeuronJ work with python.

Related tags

MiscellaneousNeuronJ
Overview

NeuronJ

This is an implementation of NeuronJ work with python. NeuronJ is a plug-in for ImageJ that allows you to create and edit neurons masks.

Why We Made It

Since we are not a neuroscientist, we wanted to make a tool that would be useful for our research, would be easy to use, and would be easy to modify. But the main reason we made it was if you want to process a lot of data and you want to create a mask for each image and save them, it could take a lot of your time with NeuronJ and ImageJ.

You may say ImageJ can be fast with scripts, But it isn't. It will not help you to do everything. So due to the lack of time, we made this.

How to use

Step 1: prepare the data

For this step, your Raw data folder should contain the following files:

For each sample:

  • sample_name.tif
  • sample_name.ndf

Notes:

  • The name of the image and mask (trace) sample should be the same as each other.
  • '.ndf' file must be in the same format as NeuronJ format.
  • This folder is your Raw data folder.

Step 2: Where to save the data

Consider where you want to save your data. Don't worry, we do all the work for you and creat folders for you. Just tell us where.

The folling folders will be created:

  • Output folder you specified
  • Output folder for images as images
  • Output folder for masks as masks
  • Output folder for image and masks together as image_mask

Notes:

  • image_mask: the mask will be on the image for show case.

Step 3: Run the script

You just need to replace the path of your Raw data folder and the output folder in the script. Our default path is:

  • Raw data folder: "./data/rawData/"
  • Output folder: "./data/dataSet/"
NeuronJ(data_addr:str, 
        output_dir:str,
        image_dir_name:str = 'images', 
        mask_dir_name:str = 'masks', 
        image_ext:str = '.tif', 
        mask_ext:str = '.tif',
        colorize:bool = True,
        show_result:bool = False)

Features

  • Save results as every image format. Default is TIFF (.tif).
  • Show the mask on the image.
  • Colorize the mask. It can be black and white or colorful.
  • Easy to modify the script as you need.
  • Perfect documentation. Easy to undrestand. Easy to use.
  • Quickly and good performance.
  • Functional with good representation.

Support

Please feel free to contact us if you have any questions. If you have any problem or idea, please leave us an issue on Github.

If you enjoyed it, I appreciate it if you bless us with your star. Thank you for your support.

To Do

  • Add some samples (.ndf files, images and masks) for represent the work.
You might also like...
Research on how Gboard Stickers work.
Research on how Gboard Stickers work.

Google-Sticker-Mashup-Research Research on how Gboard Stickers work. Contribute Contributing is nice, and you will be listed below for contributing. C

Jeremiah 45 Oct 28, 2022
Blender Light Manipulation - A script that makes it easier to work with light
Blender Light Manipulation - A script that makes it easier to work with light

Blender Light Manipulation A script that makes it easier to work with light 1. Wstęp W poniższej dokumentacji przedstawiony zostanie skrypt, który swo

Tomasz 1 Oct 19, 2021
Script to work around some quirks of the blender obj importer

ObjFix 1.0 (WIP) Script to work around some quirks of the blender obj importer Installation Download this repo In Blender, press "Edit" on the top-bar

Red_3D 4 Nov 20, 2021
This is a small compiler to demonstrate how compilers work.

This is a small compiler to demonstrate how compilers work. It compiles our own dialect to C, while being written in Python.

Md. Tonoy Akando 2 Jul 19, 2022
An attempt at furthering Factorio Calculator to work in more general contexts.

factorio-optimizer Lets do Factorio Calculator but make it optimize. Why not use Factorio Calculator? Becuase factorio calculator is not general. The

Jonathan Woollett-Light 1 Jun 3, 2022
A rough GSL work DynSAGE of my graduation project

DynSAGE Codes w.r.t DynSAGE-Diffuse can be found in function apply_dyn_model_v2 of src/utils.py. The training entrance is Line 144 - 155 of src/main.p

Yuhan Wang 3 Mar 22, 2022
A Microsoft reward automator, designed to work headless on a raspberry pi

MsReward A Microsoft reward automator, designed to work headless on a raspberry pi. Tested with a pi 3b+ and a pi 4 2Gb . Using a discord bot to log e

null 10 Dec 21, 2022
Collection of tools to be more productive in your work environment and to avoid certain repetitive tasks. 💛💙💚
Collection of tools to be more productive in your work environment and to avoid certain repetitive tasks. 💛💙💚

Collection of tools to be more productive in your work environment and to avoid certain repetitive tasks. 💛💙💚

Raja Rakotonirina 2 Jan 10, 2022
NUM Alert - A work focus aid created for the Hack the Job hackathon

Contributors: Uladzislau Kaparykha, Amanda Hahn, Nicholas Waller Hackathon Team Name: N.U.M General Purpose: The general purpose of this program is to

Amanda Hahn 1 Jan 10, 2022
Releases(v0.1.0)
Owner
Mohammad Mahdi Samei
M.Sc. student of artificial intelligence. I'm a UX strategist, data scientist, and image processing specialist. Looking forward to working with you.
Mohammad Mahdi Samei
GitHub Repository
Backup dc registry - A simple POC that abuses Backup Operator privileges to remote dump SAM, SYSTEM, and SECURITY

Backup Operator Registry Backup to Domain Compromise A simple POC that abuses Ba

Horizon 3 AI Inc 57 Dec 18, 2022
AndroidEnv is a Python library that exposes an Android device as a Reinforcement Learning (RL) environment.

AndroidEnv is a Python library that exposes an Android device as a Reinforcement Learning (RL) environment.

DeepMind 814 Dec 26, 2022
Python code to control laboratory hardware and perform Bayesian reaction optimization on the MIT Make-It system for chemical synthesis

Description This repository contains code accompanying the following paper on the Make-It robotic flow chemistry platform developed by the Jensen Rese

Anirudh Nambiar 11 Dec 10, 2022
Safely pass trusted data to untrusted environments and back.

ItsDangerous ... so better sign this Various helpers to pass data to untrusted environments and to get it back safe and sound. Data is cryptographical

The Pallets Projects 2.6k Jan 01, 2023
Black-Scholes library implemented as a Cairo smart contract

Cairo Black-Scholes Library Black-Scholes library implemented as a Cairo smart contract. All inputs, outputs, and internal calculations use 27-digit f

Aditya Raghavan 47 Dec 19, 2022
Mengzhan (John) code for Closed Loop Control system of Sharp Wave Ripples in Hippocampus CA3 region

ClosedLoopControl_Yu Mengzhan (John) code for Closed Loop Control system of Sharp Wave Ripples in Hippocampus CA3 region Creating Python Virtual Envir

Mengzhan (John) Liufu 1 Jan 22, 2022
A domonic-like wrapper around selectolax

A domonic-like wrapper around selectolax

byteface 3 Jun 23, 2022
chiarose(XCR) based on chia(XCH) source code fork, open source public chain

chia-rosechain 一个无耻的小活动 | A shameless little event 如果您喜欢这个项目，请点击star 将赠送您520朵玫瑰，可以去 facebook 留下您的(xcr)地址，和github用户名。 If you like this project, please

ddou123 376 Dec 14, 2022
A Dungeon and Dragons Toolkit using Python

Pythons-Dungeons A Dungeon and Dragons Toolkit using Python Rules: -When you are commiting please don't delete parts of the code that are important -A

2 Oct 21, 2021
VHDL to Discrete Logic on PCB Flow

PCBFlow Highly experimental set of scripts to transform a digital circuit described in a hardware description language (VHDL or Verilog) into a discre

Tim 77 Nov 04, 2022
Pokemon catch events project to demonstrate data pipeline on AWS

Pokemon Catches Data Pipeline This is a sample project to practice end-to-end data project; Terraform is used to deploy infrastructure; Kafka is the t

Vitor Carra 4 Sep 03, 2021
This tool for beginner and help those people they gather information about Email Header Analysis, Instagram Information, Instagram Username Check, Ip Information, Phone Number Information, Port Scan

This tool for beginner and help those people they gather information about Email Header Analysis, Instagram Information, Instagram Username Check, Ip Information, Phone Number Information, Port Scan.

cb-kali 5 Feb 18, 2022
Dot Browser is a privacy-conscious web browser with smarts built-in for protection against trackers and advertisments online.

🌍 Take back your privacy with Dot Browser, the privacy-conscious web browser that protects you from being tracked and monitored online.

Dot HQ 1k Jan 07, 2023
Simple, configuration-driven backup software for servers and workstations

title permalink borgmatic index.html It's your data. Keep it that way. borgmatic is simple, configuration-driven backup software for servers and works

borgmatic collective 1.3k Dec 30, 2022
Hello, Welcome to this repo. don't forget to read guidelines in readme.md

Hacktoberfest_2021 If you looking for your first contribution, we are here to help. Just create a simple program using any language you like in our fo

Wafa Rifqi Anafin 117 Dec 14, 2022
Procedural 3D data generation pipeline for architecture

Synthetic Dataset Generator Authors: Stanislava Fedorova Alberto Tono Meher Shashwat Nigam Jiayao Zhang Amirhossein Ahmadnia Cecilia bolognesi Dominik

Computational Design Institute 49 Nov 25, 2022
Custom python interface to xstan (a modified (cmd)stan)

Custom python interface to xstan (a modified (cmd)stan) Use at your own risk, currently everything is very brittle and will probably be changed in the

2 Dec 16, 2021
Blender Add-on to Add Metal Materials to Your Scene

Blender QMM (Quick Metal Materials) Blender Addon to Add Metal Materials to Your Scene Installation Download the latest ZIP from Releases. Usage This

Don Schnitzius 27 Dec 26, 2022
My Solutions to 120 commonly asked data science interview questions.

Data_Science_Interview_Questions Introduction 👋 Here are the answers to 120 Data Science Interview Questions The above answer some is modified based

Milaan Parmar / Милан пармар / _米兰 帕尔马 181 Dec 31, 2022
An open source server for Super Mario Bros. 35

SMB35 A custom server for Super Mario Bros. 35 This server is highly experimental. Do not expect it to work without flaws.

Yannik Marchand 162 Dec 07, 2022