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High-Content_Screening.html
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<!doctype html>
<html lang="en">
<head>
<title>High Content Screening</title>
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Facilities
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<h1 class="caption">
High-Content Screening
</h1>
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<h3>
An Introduction
</h3>
<p>
The High-Content Screening facility provides access to cutting edge high-throughput imaging equipment,
as well as powerful automated image and data analysis tools. This unit is a natural end point for
automated assays including large-scale RNAi/chemical screens. Our expertise in high-throughput imaging
and high-content analysis ensures the most efficient and robust screen design. The available microscopes
enable high-speed automated imaging of multi-well plates and regular microscopy slides at either low or
high resolution. Combined with advanced image analysis tools, this allows for the development of a wide
range of standard and easily customized applications applicable to multiple areas of biomedical
research.
</p>
</div>
<div class="col-md-6 col-sm-12 mt-3">
<div class="">
<img src="img/Monica_Hasegan_describing_the_BioPipeline.jpg" alt="Monica Hasegan describing the BioPipeline " width="100%">
</div>
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Quick Navigation
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Services
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Equipment
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Pricing
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Policies
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<h1 class>
Services
</h1>
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<div class="services">
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<h3>
1. High-Content Imaging
</h3>
<p>
High-Content Screening is automated image acquisition and analysis in high-throughput. It enables fast testing of many
biological conditions including arrayed genetic and chemical screens, while ensuring reproducibility and objective
quantification of images. A wide variety of different applications can be accommodated including cell counting and
morphology, colony growth tracking, drug screening, cell viability and proliferation assays, protein translocation, and
co-localization assays. Assays can be performed in multi-well format on fixed or live cells in monolayers or organoids.
Time-lapse imaging for multiple plates using plate scheduler modules is available on the BioPipeline (44 plates) and the Incucytes (6 plates).
</p>
<div class="row">
<div class="col-lg-4 col-sm-6">
<img src="img/Nikon_biopipelin-cerebral-organoid.jpg" alt="Cerebral Organoid" width="100%" style="border-radius: 0%;">
<p>
BioPipeline whole cerebral organoid embedded in a vascularized hydrogel, 4x, FITC (A. Yamand, Wrana lab, LTRI)
</p>
</div>
<div class="col-lg-4 col-sm-6">
<img src="img/Incuyte_confluency-assay.jpg" alt="Incucyte Confluency assay" width="100%" style="border-radius: 0%;">
<p>
Incucyte confluency assay, phase with segmentation mask (K. Pacholczyk, Swallow lab, LTRI)
</p>
</div>
<div class="col-lg-4 col-sm-6">
<video width="100%" controls>
<source src="img/Video/INCell_Scratch-wound-healing-assay_Phase_4X.webm" type="video/webm">
Your browser does not support the video tag.
</video>
<p>
IN Cell Scratch Wound Healing Assay - 4x magnification, phase contrast (D. Ng, Swallow Lab, LTRI)
</p>
</div>
</div>
<hr>
<h3>
2. High-Content Data Analysis
</h3>
<p>
We have several tools for automated image analysis. They include ones which can be used without extensive training to create
simple analysis algorithms (Incucyte Analysis, Celígo Analysis and Columbus), as well as software.
</p>
<h5>
NIS-Elements HC (Nikon)
</h5>
<p>
NIS-Elements HC is a total acquisition-to-analysis solution for high-content imaging applications. It streamlines high-speed,
automated multi-well plate acquisition, data review, analysis and management of multiple plate experiments. Multiple
scans can be analyzed simultaneously during the imaging phase or run post-acquisition on offline stations. Heat maps of well/plates,
sample images, binary masks, assay results, sample labels and other metadata are centralized for quick filtering, gating and
drill down to cellular detail. NIS-Elements offers histogram, scatterplot, bar chart, XY line, classification and gating
functions. Users can easily navigate within the Plate View and export to Excel or bitmap.
</p>
<h5>
Celígo Analysis (Nexcelom Bioscience)
</h5>
<p>
This built-in image analysis tool allows on-the-fly analysis of acquired images. Recommended applications include label-free cell
growth tracking, cell cycle analysis, cell viability and apoptosis, transfection optimization, multiplex fluorescent expression
assays, and many others. Once image acquisition is complete, data can be re-analyzed at an offline workstation. This instrument
is ideal for up to 4-channel imaging of multi-well plates at 4X low-resolution.
</p>
<h5>
Columbus (PerkinElmer)
</h5>
<p>
Columbus is a universal image data storage and analysis system that enables access to stored images via a standard internet browser.
The Columbus system allows scientists to remotely access, view, annotate, and analyze images. Columbus is based on an OMERO server and
therefore supports a variety of existing microscope file formats. Integrated image analysis tools are intuitive and efficient. A
high-performance computing server enables hyper-threading of image analysis. PhenoLOGIC™ machine learning technology provides an easy
way to classify cells or subcellular regions within a given data-set.
</p>
<h5>
Acapella (PerkinElmer)
</h5>
<p>
Acapella is a powerful tool for image analysis. It has a set of proprietary scripts for detection of typical cell shapes and
sub-cellular organelles. This is combined with a versatile programming environment to create customized algorithms for a
variety of biological applications.
</p>
<h5>
Matlab (Mathworks)
</h5>
<p>
Matlab is the most powerful application for advanced analysis of images. Flexible image and data handling allows highly specialized
routines for image analysis, including complex image filtering and segmentation. Costing for this analysis will be determined based on
the complexity of the analysis.
</p>
</div>
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<h1 class>
Equipment
</h1>
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<img src="img/Nikon-Biopipeline.jpg" alt="Nikon-Biopipeline" width="100%">
</div>
<div class="col-md-9 col-sm-12">
<h3>
1. Nikon BioPipeline
</h3>
<p>
The <a href="https://www.microscope.healthcare.nikon.com/products/high-content-imaging/biopipeline-live">Nikon BioPipeline</a>
is a high-end, line scanning confocal high-content platform based on Nikon’s Eclipse fully-motorized, inverted Ti2 microscope and the A1R-HD25 system.
An integrated 44-multi-well plate incubator provides multi-user assay scheduling. It is ideally suited for high-resolution fixed or live screening assays
such as detection of DNA damage foci, translocation assays, measuring of cilia lengths, co-localization studies, drug screenings or any other assay that
needs to combine high-resolution with automated imaging.
</p>
</div>
</div>
<hr>
<div class="row">
<div class="col-md-3 col-sm-12">
<img src="img/incell-analyzer-6k.jpg" alt="IN Cell Analyzer 6000" width="100%">
</div>
<div class="col-md-9 col-sm-12">
<h3>
2. IN Cell Analyzer 6000
</h3>
<p>
The IN Cell Analyzer 6000 is a laser-based, line-scanning confocal imaging platform with both widefield and confocal capabilities. This instrument is
designed for high-throughput fixed or live imaging and assay development on a variety of vessel types. It can be used for timelapse and endpoint assays
as well as 3-D imaging, co-localization studies and low signal assays.
</p>
</div>
</div>
<hr>
<div class="row">
<div class="col-md-3 col-sm-12">
<img src="img/IncucyteSx5.jpg" alt="IncucytesSX5" width="100%">
</div>
<div class="col-md-9 col-sm-12">
<h3>
3. Sartorius Incucytes
</h3>
<p>
The Incucyte platforms are automated, high-content, widefield, multi-well plate acquisition, analysis and visualization platforms designed for long live
imaging within an incubator. They offer dynamic insights into the health, viability, morphology, movement and function of cell models, with assays
including confluence monitoring, spheroid and organoid detection, and scratch-wound. Our facility has an Incucyte S3 and the latest Incucyte SX5.
</p>
</div>
</div>
<hr>
<div class="row">
<div class="col-md-3 col-sm-12">
<img src="img/Celigo.jpg" alt="Celigo" width="100%">
</div>
<div class="col-md-9 col-sm-12">
<h3>
4. Celígo
</h3>
<p>
Celígo is a low-resolution high-throughput microscope, equipped with LED-based light sources (brightfield and 3 fluorescent channels). Uniform well
illumination and large-chip CCD camera allow users to image entire wells at a high-speed. Built-in image analysis tools allow performing on-the-fly
analysis in a variety of biological applications (cell/colony counting, migrations assays, expression analysis and many others).
</p>
</div>
</div>
<hr>
<div class="equipment collapse_table">
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<i class="bi bi-arrow-down-short"></i> Detailed Specifications <i class="bi bi-arrow-down-short"></i>
</button>
</div>
<div class="collapse" id="collapseWidth1">
<table class="table-responsive table-striped table-bordered table">
<thead class="table-dark">
<tr>
<th>
</th>
<th>
Nikon BioPipeline Live
</th>
<th>
In Cell Analyzer 6000
</th>
<th>
Incucyte
</th>
<th>
Celigo
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
Type
</td>
<td>
Point-scanner confocal
</td>
<td>
Line-scanner confocal, widefield
</td>
<td>
Widefield
</td>
<td>
Widefield
</td>
</tr>
<tr>
<td>
Objectives
</td>
<td>
<li>
4X Nikon Plan Apo 0.2 NA 20 mm WD, Air
</li>
<li>
10X Nikon Plan 10X 0.45 NA 4 mm WD, Air
</li>
<li>
20X Nikon Plan Apo 0.75 NA 1 mm WD, Air
</li>
<li>
20X Nikon Apo Water 0.95 NA 0.95 mm WD, Water
</li>
<li>
20X Nikon S Plan Fluor ELWD 0.45 NA 8.2 mm WD, Air
</li>
<li>
40X Nikon Plan Apo 0.95 NA 0.17-0.25 mm, Air
</li>
<li>
40X Nikon Apo 1.15 NA 0.59-0.61 mm WD, Water
</li>
<li>
40X Nikon S Plan Fluor ELWD 0.4 NA 3.6 mm WD, Air
</li>
<li>
60X Nikon Plan Apo 1.2 NA 0.28-0.31 mm WD, Water
</li>
<li>
60X Nikon Plan Fluor Air ELWD 0.7 NA 1.8-2.6 mm WD, Air
</li>
</td>
<td>
<li>
4X Nikon Plan Apo 0.2 NA 20 mm WD, Air
</li>
<li>
10X Nikon Plan Apo 0.45 NA 4 mm WD, Air
</li>
<li>
20X Nikon Plan Fluor ELWD 0.45 NA 7.5 mm WD, Air
</li>
<li>
60X Nikon Plan Fluor ELWD 0.7 NA 1.8 mm WD, Air
</li>
</td>
<td>
<li>
4X Plan
</li>
<li>
10X Plan Fluor
</li>
<li>
20X Plan Fluor
</li>
</td>
<td>
<li>
4X
</li>
</td>
</tr>
<tr>
<td>
Excitation wavelengths
</td>
<td>
<li>
Blue 405 nm
</li>
<li>
Green 488 nm
</li>
<li>
Red 561 nm
</li>
<li>
Far-red 640 nm
</li>
</td>
<td>
<li>
Blue 405 nm
</li>
<li>
Green 488 nm
</li>
<li>
Red 561 nm
</li>
<li>
Far-red 640 nm
</li>
</td>
<td>
1st module:
<li>
Green 440-480 nm (Incucyte S3, SX5)
</li>
<li>
Red 565-605 nm (Incucyte S3, SX5)
</li>
Swappable module Incucyte
<li>
Green 453–485 nm
</li>
<li>
Orange 648-674 nm
</li>
<li>
NIR 576–639 nm
</li>
</td>
<td>
<li>
Blue 377+/-50 nm
</li>
<li>
Green 483+/-32 nm
</li>
<li>
Red 531+/-40 nm
</li>
<li>
Far-red 628+/- 40 nm
</li>
</td>
</tr>
<tr>
<td>
Non-fluorescent channels
</td>
<td>
Brightfield
</td>
<td>
Brightfield, DIC, Phase
</td>
<td>
Phase
</td>
<td>
Brightfield
</td>
</tr>
<tr>
<td>
Imaging modality
</td>
<td>
2D, 3D
</td>
<td>
2D, 3D, Maximum intensity projection
</td>
<td>
2D
</td>
<td>
2D
</td>
</tr>
<tr>
<td>
Environmental Control
</td>
<td>
Yes
</td>
<td>
Yes
</td>
<td>
Yes
</td>
<td>
No
</td>
</tr>
<tr>
<td>
Associated software
</td>
<td>
NIS Elements
</td>
<td>
Columbus
</td>
<td>
Built-in Incucyte analysis
</td>
<td>
Built-in Celigo analysis
</td>
</tr>
</tbody>
</table>
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Pricing
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<p>
Pricing is for external academic users only. Internal or industry users should contact Monica Hasegan ([email protected]) for pricing.
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<thead class="table-dark">
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<th>
HCS Instruments
</th>
<th>
Assisted
</th>
<th>
Unassisted (1st hour)
</th>
<th>
Unassisted (subsequent hours)
</th>
<th>
Offpeak<sup>1</sup> (1st hour)
</th>
<th>
Off-peak<sup>1</sup> (subsequent hours)
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<td>
Nikon BioPipeline
</td>
<td>
$99.00
</td>
<td>
$75.00
</td>
<td>
$53.00
</td>
<td>
$25.00
</td>
<td>
$16.00
</td>
</tr>
<tr>
<td>
GE IN Cell 6000
</td>
<td>
$99.00
</td>
<td>
$75.00
</td>
<td>
$53.00
</td>
<td>
$25.00
</td>
<td>
$16.00
</td>
</tr>
<tr>
<td>
Celígo
</td>
<td>
$99.00
</td>
<td>
$30.00
</td>
<td>
$21.00
</td>
<td>
$10.00
</td>
<td>
$6.00
</td>
</tr>
</tbody>
</table>
<p>
<u><sup>1</sup>Peak hours are Monday to Friday, 9:00 AM to 6:00 PM</u>
</p>
<br>
<table class="table table-striped table-bordered table-responsive">
<thead class="table-dark">
<tr>
<th>
Incucytes
</th>
<th>
External Pricing ($/plate/day)
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
Essen Incucyte SX5
</td>
<td>
$110.00
</td>
</tr>
<tr>
<td>
Essen Incucyte SX3
</td>
<td>
$110.00
</td>
</tr>
</tbody>
</table>
<hr>
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<thead class="table-dark">
<th colspan="3">
External Pricing ($/hr)
</th>
</tr>
<tr>
<th>
Software
</th>
<th>
Assisted
</th>
<th>
Unassisted
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
Image Analysis Workstation
</td>
<td>
$99.00
</td>
<td>
$12.00
</td>
</tr>
</tbody>
</table>
<hr>
<table class="table table-striped table-bordered table-responsive">
<thead class="table-dark">
<tr>
<th>
Assisted Use
</th>
<th>
External Pricing ($/hr)
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
Training/Theory/Data Analysis/Assay Development
</td>
<td>
$99.00
</td>
</tr>
</tbody>
</table>
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<h1 class>
Policies
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<h3>
Accessing the Facility
</h3>
<p>
<li>
Users interested in accessing the High-Content Screening Facility should contact Monica Hasegan ([email protected]) to discuss the scope of their project.
</li>
</p>
<hr>
<h3>
Getting Started
</h3>
<p>
<li>
All new users must review our <a href="assets/PDF/hcs/HCS_getting_started_guide.docx">getting started guide</a>. To work unassisted, users must first complete training with the facility manager.
</li>
</p>
<hr>
<h3>
Biosafety
</h3>
<p>
<li>
Users who plan to do live cell imaging experiments have to meet with the manager to discuss potential bio-safety risks and to ensure appropriate training. Users must be familiar with practices outlined in Laboratory Biosafety Guidelines (3rd edition, 2004, Public Health Agency of Canada-PHAC and enforced by the human Pathogens and Toxins act).
</li>
</p>
<hr>
<h3>
Data Management
</h3>
<p>
<li>
Data storage is the sole responsibility of the client and clients are urged to transfer data to their own storage devices as soon as possible. Data will be removed regularly from the instrument workstation since it adversely affects instrument performance.
</li>
<li>
Data storage on the dedicated analysis workstations will be removed when necessary (and without notice), so please use access to the LTRI network drives available on the analysis workstations to save your data or store directly to external storage devices.
</li>
</p>
<hr>
<h3>
Acknowledgement
</h3>
<p>
Preferred acknowledgment for the Network Biology Collaborative Centre High-Content Screening Facility:
<br>
<b>
The authors wish to thank [staff name] of the Network Biology Collaborative Centre High-Content Screening Facility (RRID: SCR_025391) at the Lunenfeld-Tanenbaum Research Institute for [service]. The facility is supported by the Canada Foundation for Innovation and the Ontario Government.
</b>
<br><br>
Click here for our <a href="resources.html">publication policy</a> and preferred acknowledgement for other NBCC Facilities.
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