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. Wstฤ™p W poniลผszej dokumentacji przedstawiony zostanie skrypt, ktรณry 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. ๐Ÿ’›๐Ÿ’™๐Ÿ’š
Collection of tools to be more productive in your work environment and to avoid certain repetitive tasks. ๐Ÿ’›๐Ÿ’™๐Ÿ’š

Collection of tools to be more productive in your work environment and to avoid certain repetitive tasks. ๐Ÿ’›๐Ÿ’™๐Ÿ’š

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
A beautiful and useful prompt for your shell

A Powerline style prompt for your shell A beautiful and useful prompt generator for Bash, ZSH, Fish, and tcsh: Shows some important details about the

Buck Ryan 6k Jan 08, 2023
0xFalcon - 0xFalcon Tool For Python

0xFalcone Installation Install 0xFalcone Tool: apt install git git clone https:/

Alharb7 6 Sep 24, 2022
Very Simple 2 Message Spammer!

Very Simple 2 Message Spammer!

Syntax. 4 Dec 06, 2022
A collection of resources on neural rendering.

awesome neural rendering A collection of resources on neural rendering. Contributing If you think I have missed out on something (or) have any suggest

1.8k Dec 30, 2022
Blender addon to import images as meshes

ImagesAsMesh Blender addon to import images as meshes. Inspired by: ImagesAsPlanes Installation It's like just about every other Blender addon. Downlo

Niccolo Zuppichini 4 Jan 04, 2022
A program that lets you use your tablet's tilting to emulate an actual joystick on a Linux computer.

Tablet Tilt Joystick A program that lets you use your tablet's tilting to emulate an actual joystick on a Linux computer. It's called tablet tilt joys

1 Feb 07, 2022
A way to write regex with objects instead of strings.

Py Idiomatic Regex (AKA iregex) Documentation Available Here An easier way to write regex in Python using OOP instead of strings. Makes the code much

Ryan Peach 18 Nov 15, 2021
A micro-service that can be extended to help in monitoring systems

A micro-service that can be extended to help in monitoring systems. Be extensible to be incorporated in any of the systems to facilitate timely interventions.

Peter Kagwe 1 Feb 06, 2022
Modify version of impacket wmiexec.py, get output(data,response) from registry, don't need SMB connection, also bypassing antivirus-software in lateral movement like WMIHACKER.

wmiexec-RegOut Modify version of impacket wmiexec.py,wmipersist.py. Got output(data,response) from registry, don't need SMB connection, but I'm in the

ๅฐ็ฆป 228 Jan 04, 2023
Buffer overflow example for python

Buffer overflow example for python

Mehmet 1 Jan 04, 2022
Transform your boring distro into a hacking powerhouse.

Pentizer Transform your boring distro into a hacking powerhouse. Pentizer is a personal project that imports Kali and Parrot repositories in any Debia

Michail Tsimpliarakis 2 Nov 05, 2021
A simple service that allows you to run commands on the server using text

Server Text A simple flask service that allows you to run commands on the server/computer over sms. Think of it as a shell where you run commands over

MT Devs 49 Nov 09, 2021
Our Ping Pong Project of numerical analysis, 2nd year IC B2 INSA Toulouse

Ping Pong Project The objective of this project was to determine the moment of impact of the ball with the ground. To do this, we used different model

0 Jan 02, 2022
Python scripts to interact with Upper Deck ePack online trading card platform

This script should connect to the Upper Deck ePack API using your browser cookies and download a list of your current collection and save it as a CSV.

Adrian Kent 1 Nov 22, 2021
Create Arrays (Working with For Loops)

DSA with Python Create Arrays (Working with For Loops) CREATING ARRAYS WITH USER INPUT Array is a collection of items stored at contiguous memory loca

1 Feb 08, 2022
Open source stenotype engine

Plover Bringing stenography to everyone. Homepage Releases Wiki Blog Google Group Discord Chat About Installation Getting help Contributing Donations

Open Steno Project 2k Jan 09, 2023
Python tools for working with Orbit Ephemeris Messages (OEMs).

Python Orbit Ephemeris Message tools Python tools for working with Orbit Ephemeris Messages (OEMs). Development Status Installation The oem package is

Brad Sease 4 Apr 06, 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
A light library to build tiny websites

A light library to build tiny websites

BT.Q 1 Dec 23, 2021
The bidirectional mapping library for Python.

bidict The bidirectional mapping library for Python. Status bidict: has been used for many years by several teams at Google, Venmo, CERN, Bank of Amer

Joshua Bronson 1.2k Dec 31, 2022