Experimental Systems & Tools
Experimental Systems & Tools
Embedded Files
Imaging Systems
Imaging Systems
Our lab has two home-built confocal microscopes based on Motorized AxioObserver.Z1 AxioObserver.Z1 inverted microscopes with provisions for very long term, automated multisite, multicolor laser scanning imaging
The systems are equipped with robotic stages, autofocus systems, headstages for simultaneous electrophysiogical recordings via Multielectrode Array (MEA) dishes, and home built life support systems (slow perfusion, 5% CO2, heating) designed and built by Vladimir Lyachov and Leonid Odessky.
The systems are controlled by software written in C and C++ by Noam Ziv.
A third system is under construction.
In addition, the lab is equipped with an upright Zeiss microscope equipped with an Andor EMCCD camera. The system was recently adapted for concomitant imaging of- and recording from high density MEAs
A time lapse of a developing dendrite captured every 10 minutes for about 1 week using one of our home-built confocal microscopes. The neuron, expressing PSD-95 fused to EGFP, was plated on a thin-glass MEA dish which was connected to a slow perfusion system and maintained in an atmospheric environment of 5%CO2 at approximately 37 degrees centigrade.
Images collected by Dr. Amir Minerbi, are from "Long-Term Relationships between Synaptic Tenacity, synaptic remodeling, and network activity"
Multielectrode Array (MEA) recording systems
Multielectrode Array (MEA) recording systems
Our lab has four systems for 60 electrode MEA dishes - for recording and stimulation. The systems are based on MultichannelSystems MEA-1060 headstages, connected to home-built electronics, and a 64 channel A/D boards (Adlink DAQe-2204 or UEI Power DAQ PD2-MF-64-3 M/12H/L on older systems)
Recording and stimulation is controlled using a software application (CLEM- Closed loop Experiment Manager") written in C and C++ by Hananel Hazan and Noam Ziv.
The software includes provisions for recording, logging, stimulating and running closed-loop experiments using short plug-in routines.
Two of the systems in our lab are combined with imaging systems, and two are stand-alone MEA systems
In addition, the Ziv lab created large libraries of analysis routines written in Matlab and C-based DLLs for analyzing data generated by these systems.
Activity recorded from a network of mouse cortical neurons growing on a 60-electrode thin glass MEA using CLEM, the recording and stimulation system developed in house. The right side shows individual action potentials recorded from individual electrodes. The matrix illustrates firing rates at each electrode whereas the bottom panel provides raster plots of action potentials and firing rates across all electrodes.
More information on this system can be found in "Closed Loop Experiment Manager (CLEM)—An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments"
Image Analysis Software
Image Analysis Software
The major tool used in our lab for image analysis is Openview, a software application developed over many years according to changing needs. The application, written in C and C++ is focused on the analysis of 6D image stacks (x,y,z, time, channel and site).
The software has built in provisions for image alignment, extended focus (projection), movie generation, 3D object detection and automated tracking, intensity measurements, colocalization, data logging and more.
Furthermore, the software has provisions for inclusion of external image processing routines ('plug-ins') and provides an OLE Automation interface for controlling it from other programs such as Excel, Matlab and Python (a custom Toolbar for Excel is available)
Tracking synapses expressing with PSD-95:mTurquoise2 (green) and mCitrine:GKAP (red) using Openview. Rectangular Areas of Interest (AOIs) were placed programmatically on punctate fluorescent objects and then tracked automatically through the time lapse series. Tracking is automatic, but as errors occur occasionally, users can easily intervene by dragging the AOI to the correct location, after which tracking continues from the corrected position.
In the analysis of this time series (in which images were taken at one hour intervals) tracking was 'locked' to the green (PSD-95) channel. Objects that split or merged were omitted. Tracking was carried out on projections of all Z sections, but tracking can be also carried out in 3D.
Images credit - Nadia Blom
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