μManager is a software package for control of automated microscopes. Together with the image processing application ImageJ, μManager provides a comprehensive, freely available, imaging solution.

μManager has a simple and clean user interface, through which it lets you execute common microscope image acquisition tasks such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. μManager works with microscopes from all four major manufacturers (Leica, Nikon, Olympus and Zeiss), most scientific-grade cameras and many peripherals (stages, filter wheels, shutters, etc.) used in microscope imaging (check the list of supported hardware).

Calcium imaging analysis made easy. EZcalcium is a flexible, user-friendly toolbox for analysis of calcium imaging data, controlled by a set of intuitive graphical user interfaces (GUI) based on MATLAB.

Components & general workflow

EZcalcium contains three main modules: Motion Correction, ROI Detection, and ROI Refinement. Typically, an imaging data file is processed through this workflow.

• Motion Correction, based on the NoRMCorre toolbox, applies image alignment to correct for motion artifacts in the raw imaging data.
• ROI Detection, based on the CaImAn toolbox, performs automated ROI detection, signal extraction, and deconvolution of fluorescence calcium signals.
• ROI Refinement enables the user to inspect detected ROIs, manually exclude ROIs, and use automated, customized ROI exclusion criteria, including spatial and activity-dependent metrics.

Step-by-step instructions for using each module can be found on the EZcalcium GitHub Wiki page.

NeuroRighter is an open-source system for multi-electrode closed-loop recording and stimulation.  It was originally produced by the Potter Lab at Georgia Tech, and has enabled pioneering neuroscience research through precise electrical and optical control of neural tissue. The software is free, and the hardware schematics and layouts are free for download. This site contains 'living' documentation for the system, describing its use and construction.

SIMA (Sequential IMage Analysis) is an Open Source package for analysis of time-series imaging data arising from fluorescence microscopy. The functionality of this package includes:

• correction of motion artifacts
• segmentation of imaging fields into regions of interest (ROIs)
• extraction of dynamic signals from ROIs

The included ROI Buddy software provides a graphical user interface (GUI) supporting the following functionality:

• manual creation of ROIs
• editing of ROIs resulting from automated segmentation
• registration of ROIs across separate imaging sessions

Link to the Github repository

OMERO : 

From the microscope to publication, OMERO handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software. Over 140 image file formats supported, including all major microscope formats.

Bio-Formats: 

Bio-Formats is a software tool for reading and writing image data using standardized, open formats. Bio-Formats is a community driven project with a standardized application interface that supports open source analysis programs like ImageJ, CellProfiler and Icy, informatics solutions like OMERO and the JCB DataViewer, and commercial programs like Matlab.

OME Files: 

OME Files is a reference implementation of the OME data model and the OME-TIFF file format for developers who wish to integrate support for the OME data model and reading and writing the standard OME-TIFF file format into their software. Potential uses include export of images using OME-TIFF, saving of acquired image data in OME-TIFF, reading metadata and image data from OME-TIFF for visualization and analysis, or use of the data model metadata APIs for handling metadata.

The OpenStage is a publication from 2014 by Robert A. A. Campbell , Robert W. Eifert, Glenn C. Turner, which gives a DIY solution to build your own microscope stage:

Abstract

Recent progress in intracellular calcium sensors and other fluorophores has promoted the widespread adoption of functional optical imaging in the life sciences. Home-built multiphoton microscopes are easy to build, highly customizable, and cost effective. For many imaging applications a 3-axis motorized stage is critical, but commercially available motorization hardware (motorized translators, controller boxes, etc) are often very expensive. Furthermore, the firmware on commercial motor controllers cannot easily be altered and is not usually designed with a microscope stage in mind. Here we describe an open-source motorization solution that is simple to construct, yet far cheaper and more customizable than commercial offerings. The cost of the controller and motorization hardware are under $1000. Hardware costs are kept low by replacing linear actuators with high quality stepper motors. Electronics are assembled from commonly available hobby components, which are easy to work with. Here we describe assembly of the system and quantify the positioning accuracy of all three axes. We obtain positioning repeatability of the order of 1um in X/Y and 0.1 um in Z. A hand-held control-pad allows the user to direct stage motion precisely over a wide range of speeds (0.1 to 100 um/s), rapidly store and return to different locations, and execute “jumps” of a fixed size. In addition, the system can be controlled from a PC serial port. Our “OpenStage” controller is sufficiently flexible that it could be used to drive other devices, such as micro-manipulators, with minimal modifications.

The PulsePal is a publication from 2014 by Joshua I. Sanders and Adam Kepecs, which gives a DIY solution to build your own open and inexpensive (~$210) alternative to pulse generators used in neurophysiology research.

Abstract 

Precisely timed experimental manipulations of the brain and its sensory environment are often employed to reveal principles of brain function. While complex and reliable pulse trains for temporal stimulus control can be generated with commercial instruments, contemporary options remain expensive and proprietary. We have developed Pulse Pal, an open source device that allows users to create and trigger software-defined trains of voltage pulses with high temporal precision. Here we describe Pulse Pal’s circuitry and firmware, and characterize its precision and reliability. In addition, we supply online documentation with instructions for assembling, testing and installing Pulse Pal. While the device can be operated as a stand-alone instrument, we also provide application programming interfaces in several programming languages. As an inexpensive, flexible and open solution for temporal control, we anticipate that Pulse Pal will be used to address a wide range of instrumentation timing challenges in neuroscience research.

Github repsitory : https://github.com/sanworks/PulsePal

3Dneuro made it available for everyone to use a good standardized tool for light shielding.

This system was designed to provide simple and reliable light shielding for 2-photon imaging in awake head-fixed mice (running on a 3D-treadmill with visual stimulation in our case). With this in mind, we optimized for the following criteria:

1. No hand-made or improvised components that can add variability to the data quality of each experiment – so no putty, wax or tape.
2. Simple connection between the animal’s headplate and the light shielding around the microscope lens, to prevent having to work close to the animal’s head, which can stress animals and impact task performance.
3. Quick fastening mechanism (< 1 minute). Animals only have a limited time span for motivated, focused performance. We want to lose as little as possible of that time on setting up the imaging. Ideally, the time between putting the animal on the treadmill and beginning the first imaging sequence should be well below 10 minutes.
4. Easy to ensure watertight seal with the skull to prevent leakage of fluid during imaging.
5. Cheap and easy to replace/tweak if necessary.

More than a century ago, Ramón y Cajal provided a qualitative description of neuronal branching in all its forms and variants. However, even today, few rigorous and useful formalisms are available for a quantitative description of dendritic and axonal morphology.

The TREES toolbox provides:

-Tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees.

-The basic tools to edit, visualize, and analyze dendritic and axonal trees.

-Methods for quantitatively comparing branching structures between neurons.

-Tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance.

This software package is written in Matlab, the most widely used scientific programming language. We hope that other groups will benefit from this package and that they will add their own code to the TREES toolbox based on their own specific applications.

Pack I/O is a data acquisition Labview software that uses National Instruments DAQ hardware to handle multiple analogue and digital signals. The software is useful for any experiment requiring acquisition and generation of data and can be triggered in several modes.

Dr. Adam Packer the developer of the product: 

"During graduate school, I was making electrophysiological recordings and trying to synchronize various pieces of equipment (cameras, lasers, galvanometers, etc.). I found no software that was up to the task so I began a project to develop an uber-system capable of performing any data acquisition or generation operation that could be completed with the National Instruments DAQ hardware in use at the Yuste lab at the time. I jokingly referred to the project as “PackIO”, a combination of my name and IO, as in input/output, as the software is supposed to be able to take any input or generate any output in any synchronized fashion. The name stuck and now PackIO is in use by members of Rafael Yuste’s laboratory, Jason Maclean’s laboratory, Roberto Araya’s laboratory, and I continue to use PackIO in Michael Hausser’s laboratory."

Link to the GitHub repository