News & Events


LS&E Day for Image Processing & Analysis

On Dec. 25th @ Room 300 Biotechnology & Food Eng., Technion

09:00-09:15 Gathering & coffee

09:15-09:30 LS&E infrastructure overview

09:30-11:00 Introduction to image processing & analysis

11:00-11:20 Coffee break 11:20-12:00 Advanced de-convolution (Dr. Douglas Lutz)

12:00-12:50 Image analysis tools (Fiji, Ilastik, Imaris, CellProfiler) & applications

12:50-13:00 Summary & New @ The LSE

Registration is needed. Please register here LSE DAY for IA .
For more information, please contact Dr. Yael Lupu Haber: , 1386



Single Cell workshop at the Technion Genome Center

Dear all,

We are happy to invite you to a Single Cell Sequencing Applications Workshop at the Technion Genome Center.

The workshop will take place on February 27th, at the Technion, Faculty of Biology, Auditorium.

Please find enclosed the program.

Technion Genome Center Single Cell Workshop

Participation is free but registration is required.

Please register here.

For more information, please contact Dr. Tal Katz-Ezov, 04-8295168,

The TGC team




Save the Date – LSE Open Day – 31.1.19

Dear all,

The LS&E Infrastructure invites you to an “Open Day”, on January 31st 2019.

 Where? Faculty of Biology, Auditorium

 When? January 31st 2019 at 09:15

 Program as a pdf file available here

 In this open day, we will present the various applications available at the LS&E infrastructure center.

 After the presentation, there will be a tour in the center’s units.

  We encourage everyone to come, in particular,  lab managers and new students, so please forward this mail to them.

 Registration to this open day, and the tour is needed. Please register here.

 Looking forward to seeing you all,

 Maayan and the LSE team


The LS&E and BCF Workshop on Light Microscopy and Image Processing & Analysis

We are happy to invite you to a joint BCF/LS&E imaging workshop.

Day 1: Monday, December 3, 2018

Location: Seminar Room, Mezzanine, Faculty of Medicine

Light Microscopy

09:00-12:00 Theoretical Instruction

Transmitted light. Fluorescence: Widefield and Confocal

Maya Holdengreber

Field Application Specialist, BCF

 12:00-12:45, Lunch break

12:45-13:45 High End Applications – BCF

Introduction to Bioimaging Center – BCF

Edith Suss-Toby

Director, Bioimaging Center, BCF

LSM880 confocal for high resolution high speed & spectral imaging

Maya Holdengreber

Field Application Specialist, BCF

Incucyte – High Throughput Live Cell Analysis System

Melia Gurewitz

Field Application Specialist, BCF

13:45-14:00, Coffee break

14:00-15:00 High End Applications – LS&E

Light Sheet Microscopy for 3D Imaging of live or fixed samples

Nitsan Dahan

Director, Microscopy & Imaging, LS&E, Technion

Incell 2000 for high content imaging and analysis

Yael Lupu-Haber

Imaging & Bioanalysis specialist, LS&E

Image stream  – to see behind the dot

Efrat Barak

Flow Cytometry Head, LS&E


Day 2: Tuesday, December 4, 2018

Location: Computer Farm, First Floor, Faculty of Biology

Image Processing & Analysis

09:00-10:15 The Numbers Behind the Image

Yael Lupu-Haber

Imaging & Bioanalysis specialist, LS&E

10:15-12:15 Imaris Basic, Hands-on

12:15-13:00, Lunch break


13:00-14:00 Image Analysis Applications

Yulia Fridman

Research Fellow, Sigal Savaldi-Goldstein Lab, Faculty of Biology

Yonit Maroudas-Sacks
PhD student, Kinneret Keren Lab, Faculty of Physics

Itai Ehrlich

Image Analysis Specialist, BCF


14:00-14:15, Coffee break


14:15-16:00 Imaris Advanced, Hands-on


Day 3: Monday, December 17, 2018

Location: Purple Computer Farm, Gallery Floor, Faculty of Medicine

13:00-16:00 FIJI Software, Hands-on


This workshop is free of charge, however, registration is required


December 4th, 2017 – 5th Israeli ImageStream user meeting

Dear LSE Users,

We would like to invite you to the 5th Israeli ImageStream user meeting taking place in Bar Ilan University on 4/12/2017.

Looking forward to seeing you there,

The LS&E Flow Cytometry team.

5th Israeli ImageStream user meeting





























November 8th, 2017 – LS&E Infrastructure Center Users Symposium

The LS&E Infrastructure Center happy to the invites You to attend a special LS&E Users Symposium day.

Date: Wednesday, Nov 8th, 10:00 o’clock,

Location:  Biology faculty auditorium, Technion


Session I: Yarden Golan, Bea Kaufmann, Moran Hod Marco & Leon Anavy

Session II: Mor Goldfeder, Roni Hass, Boris Shneyer & Noa Ben-Asher.

Session III: Despina Soteriou, Yulia Fridman & Nitzan Krinsky.


15:30 – End of Symposium

This symposium is free of charge, however, registration is required using this link.

Looking forward to seeing you all,

LSE Infrastructure Center team


July 7th, 10:00 – Special seminar on Imaging Flow Cytometry (IFC) using the Image Stream

The LS&E Flow Cytometry unit the invites You to attend special seminar on “Imaging Flow Cytometry (IFC) using the Image Stream“.

Date: Wednesday, July 7th, 10:00 o’clock,

Location:  Biology faculty auditorium, Technion

Speaker: Dr. Yael Lupu-Haber, LSE application specialist for the Image Stream

Title: Imaging Flow Cytometry (IFC) using the Image Stream


IFC combines speed, sample size and phenotyping abilities of flow cytometry with the morphological analysis ability of microscopy in a single instrument platform. It allows statistical analysis of cellular morphology, fluorescent intensity and texture.
IFC applications include:
Cell signaling, Internalization ,Co-localization ,Microbiology ,Cell cycle ,Apoptosis ,Shape change ,Cell-cell interactions ,Oceanography.

Looking forward to seeing you all,

LSE Flow Cytometry team

June 28th, 13:00 – Special seminar on IN Cell Analyzer – New platform to meet your High Content Analysis needs

The LS&E Microscopy core facility the invites You to attend special seminar on “IN Cell Analyzer – New platform to meet your High Content Analysis needs“.

Date: Wednesday, June 28th, 13:00 o’clock, (45 min’s talk)

Location:  Biology faculty auditorium, Technion

Speaker: Dr. Przemysaw Fleszar, Application Specialist, Cell Analysis, GE Healthcare

Title: IN Cell Analyzer – New platform to meet your High Content Analysis needs


Recent developments in the IN Cell portfolio enable powerful high content analysis (HCA) capabilities on live cell assays, using widefield deconvolution, line scan confocal and transmitted light imaging modalities. These cutting edge hardware platforms use class leading technologies in concert with sensitive and powerful image analysis platforms to give the user the statistical power to address biological questions in cell biology that previously lay out of reach. Results on the microscopic scales ranging from tissues, cell populations down to single cells, investigating molecular organization of individual cells in even the most sensitive of live samples.
We will present GE Healthcare’s latest advances in high content imaging technologies, integrated into the new IN Cell Analyzer platforms and our new easy-to-use IN Carta analysis software package. During the session, we will present how to automate image acquisition processes and how to quickly and confidently extract multi-parameter data from these images, regardless of prior experience levels.

Looking forward to seeing you all,

LSE Microscopy team


April 25th, 10:30 – Seminars on Clearing methodologies for biological samples

The LS&E Microscopy core facility the invites You to attend special seminars in Advanced Microscopy Application and Methodologies.

The next seminars will be on “Clearing methodologies for biological samples“.


Date: Tuesday, April 25th, 10:30 o’clock, (45 min’s talk)

Location:  Room 4-17, Emersson Building

Speaker: Shlomi Lazar, Ph.D.

Division of medical chemistry, The Israel institute for Biological Research (IIBR).

Title: Looking inside the organs: a comparative analysis of three methods for establishing optically transparent samples



Typical histological study, using sectioning of the tissue, has major limitations in obtaining 3D images of structural components and cells distribution within tissues. Ideally, samples should be imaged at high spatial resolution with minimal sectioning. However, thick tissue imaging is limited mostly because of light scattering. In this study, we compared the efficacy of three recently published clearing protocols (Scale, 3DISCO and Clarity) in generating a transparent thick section which can be subjected to confocal analysis.
Brains, ovaries and embryos obtained from transgenic mice expressing enhanced yellow fluorescent protein (eYFP) in specific cells or wild type mice, were collected and cut to thick sections (2-3mm). Some slices were first fluorescently immunolabeled for various markers. All sections were processed in one or more of the following protocols: (a) The Scale protocol was based on aqueous reagent that renders biological samples optically transparent and completely preserves fluorescent signals in the clarified structures; (b) 3DISCO (3D imaging of solvent cleared organ) was based on organic solvents that dissolve the lipid structure in the tissue and (c) The Clarity protocol was based on hydrogel tissue embedding, lipid extraction in aqueous solution, and clearing. All sections were subjected to confocal analysis. Data acquired was processed using ImageJ software.
We successfully optimized immunofluorescence labeling protocol for floating thick sections (2-3mm). Evaluation of the clear tissues produced by each of the three methods showed that Scale protocol resulted in fragile and only slightly cleared sections. 3DISCO method demonstrated transparent slices but a degraded fluorescent signal over time (1 day half-life). Thick slices processed by Clarity protocol were nicely transparent, maintained their fluorescence intensity, but were greatly more expensive. A combination of Clarity and Scale protocols replacing the high cost clarity reagent with Scale solution, improved the outcome of Scale protocol and preserved the required fluorescence intensity. All slices were successfully analyzed using confocal microscope and no further sectioning was needed.
A combined protocol of Clarity and Scale provide a low cost and available way to generate transparent organs. This enabled detailed analysis of structural and molecular information from thick organ samples.



Date: Tuesday, April 25th, 11:30 o’clock, (20 min’s talk)
Location:  Room 4-17, Emersson Building
Speaker: Nadav Yayon, M. Sc
PhD student at Prof. Hermona Soreq’s lab, The Edmond and Lily Safra Center of Brain Science. The Hebrew University of Jerusalem
Title: Extracting micro-scale features from macro-scale imaging of iDISCO brains


Recent technological advancements enable rendering samples transparent and imaging huge areas of tissue rapidly and in high resolution. However, while these technologies produce beautiful images and 3D movies, extracting quantitative information from such experimental samples is confronted with significant difficulties, both due to sample preparation procedures and because of imaging and analysis constraints. In my talk, I will share my personal experience of using the iDISCO clearing approach and Light-sheet imaging, and will describe our attempts to accurately extract 3D information to identify the location, density and morphology of cortical interneurons in the mouse cortex.


Light refreshment will be served before the seminar

Registration below is free of charge but required due to limited place. 

Looking forward to seeing you all,

LSE Microscopy team

Microscopy seminar series

March 21st, 10:00 – Seminar on Insights into super-resolution

The LS&E Microscopy core facility the invites You to attend special seminars in Advanced Microscopy Application and Methodologies.

The next seminar will be on “Insights into super-resolutionmethodologies and applications of super-resolution microscopy “.

Date: Tuesday, March 21st, 10:00 o’clock

Please keep note that the seminar will be 30 minutes earlier than the original plan.

Location: Auditorium , Faculty of Biology

Speaker: Avi Jacob, Ph.D.

Head of Light Microscopy facility, Bar-Ilan University.



Microscopy-based methods for breaking diffraction limited resolution are collectively known as super-resolution (SR). There are several methods which can be divided into two main approaches: deterministic and stochastic. Stochastic methods include all localization techniques such as STORM and deterministic methods include the optical approaches such as STED. STED (STimulated Emission Depletion) is a mature technology, yet can require optimization to reach ~50nm resolution. Recently, companies have begun to offer “hardware-optimization + software based SR”, whereby a measure of SR is achieved by automatically optimizing acquisition and then submitting to deconvolution. Each has their advantages.
Model systems need to be appropriate for SR, such as sub organelle structures, nuclear pores or fine membrane studies. Also, care must be taken to ensure that SR is technically possible taking into account the specific SR method used. For example, with STED, it’s possible the antibody-secondary-antibody tree could be larger than the airy disk. A balance must be struck between the more time consuming, yet higher resolution STED, and the faster “middle of the way” approach that can be universally used.

Light refreshment will be served before the seminar

Looking forward to seeing you all,

LSE Microscopy team