Colony Imaging with powerful Analysis Software

Transcription

1 TM Imaging with powerful Analysis Software TM Accurate Compact Fast

2 We re not going to interpret your results, but we ll do everything to get you there From image acquisition to data visualisation, straight out of the box.

3 Introduction What is it? What does it do? The PhenoBooth is a fast, semi-automated plate reader for cell colony imaging. PhenoSuite is powerful and easy-to-use colony identification and analysis software. Its modular open-architecture offers preconfigured or fully-customisable workflows and data import/export at any stage. The PhenoBooth takes a high-resolution image of colonies on any number of plates, and then PhenoSuite automatically batch-analyses all of those plates through: Image Pre-processing, Measurement, Normalisation, Analysis and Visualisation, with a single-click. Application specific software packages, such as SGA Analysis or Counting totally eliminate the tedium of any-scale image analysis in replicate. PhenoSuite filtering feature. What can I Imaging of standard sbs plates, Singer PlusPlates use it for? and 90mm petri dishes. counting picking when used with the ROTOR / Stinger. Click to see how Automatic colony feature measurement including: size, brightness, circularity and colour Automated normalisation and analysis of SGA data How does it work? The PhenoBooth contains a scientific grade camera and top and bottom SpectraStar TM flat-field illumination technology, which produces high-resolution colony images every time. The powerful PhenoSuite software accurately counts and measures the selected colony features and can be customised with different packages to automate your entire analysis, visualisation and export format.

4 Hardware Features Fluorescence The PhenoBooth is extremely quick and easy to use. Its outstanding image quality makes it an invaluable tool for colony time-lapse imaging. Gudjon Olafsson MRC National Institute for Medical Research Back light Integrated SpectraStar TM back light for high-fidelity, flat-field, transmitted light images. Filter tray PhenoBooth accepts two standard 25mm circular filters with a maximum height of 5mm Function light Light indicator to signal operation type. FLUORESCENCE FILTERS The PhenoBooth can detect fluorescence. Screening for fluorescence on agar is advantageous because it is cost-effective and very high throughput (>6,000 colonies on an SBS plate). Please contact sales@ to see if your favourite fluorescent marker is now supported. The PhenoBooth accepts standard 25 x 5mm filters in a two-position filter cartridge. The filters can be selected on a manual sliding mechanism. You can easily switch between two of your favourite image modes. Input tray Rectangular SBS plate tray with optional petri dish adaptor. Top light Integrated SpectraStar TM top light for high-fidelity, flat-field incident light images. USB 3.0 Connections for computer interface.

5 Software Features counting sizing Choosing your software package circularity PhenoSuite colony growth analysis of a petri dish. imaging should be easy... its just measuring stuff. Choose what you want to measure and let PhenoSuite do the rest. Normalisation & scoring for SGA or Y2H Customise software Accurate at 6k Export.csv for single colony picking Colour & Fluorescence Spectrastar top & bottom flat-field illumination Automatic data storage & management PhenoSuite Software capabilities PhenoSuite software uses Singer s signature easy-touse interface to automatically and accurately measure many colony properties. PhenoSuite is powerful yet flexible, offering a variety of custom-made packages to automate your entire analysis workflow. Confused by existing colony analysis software? You'll love PhenoSuite! Image acquisition at 2800x1900 with a pixel size of 45µm. Full control of imaging parameters including (but not limited to): brightness, gain, exposure, saturation, hue, contrast and white balance. Open architecture design. Compatibility for LIMS integration. separation >= 1 pixel. detection for all colonies >= 1x1 pixel. Automatic elimination of overgrown colonies. Automatic, fully customisable colony detection. Adjustable filters to remove detected objects based on size. Map colonies to genes via a gene map. Data provided on colonies includes position, size, circularity, colour, intensity and gene name. Accurately analyse colonies at 6k density. Automated normalisation and SGA analysis. Compare colony growth between plates and visualise change as heat maps. Automatic software updates with a valid PhenoSuite licence. Fluorescence: Image with UV and quantify size, colour and intensity. One-click colony analysis

6 Software Packages Picking Package Packages PhenoSuite is available with a range of different packages for different scientific applications. A package is a set of plug-ins (or functionalities) specifically grouped to streamline analysis for a particular application. This means that you get: a high-performance piece of software tailored to your experiments; you are not paying for unnecessary functionalities; and you have the options to extend the capability of your PhenoSuite by adding new plug-ins. Basic package ( Counting) Advanced packages PhenoSuite comes pre-installed with the Counting Package: Image acquisition Capture plate images using a PhenoBooth or import an existing image. SBS / Petri plate support Supports the analysis of images taken from SBS-format plates and 90mm petri dishes Cropping - Remove the edges of the plate. Background substraction - Remove the background leaving only the colonies. identification / counting - Detect the number of colonies. Exporting CSV / images - Export basic plate information If simple image processing and SBS format or 90mm petri colony counting is all you need then the basic PhenoSuite package will suffice. However, if you are doing screening experiments that require advanced analysis workflow, we have packages with specific plugins tailored to some of the most common genetic and protein interaction screens. The PhenoBooth is an integral part of our complete colony-picking platform, which also includes the ROTOR and Stinger, read more here. After the PhenoBooth captures an image of colonies, PhenoSuite automatically identifies colonies of interest based on user-defined criteria such as size, colour, circularity, and fluorescence. It then communicates the coordinates of the selected colonies to the ROTOR, allowing the Stinger to pick those colonies into multi-well plates. Plug-in Size Circularity Counting Upgrade available Picking Package SGA Y2H Random mutagenesis Screens Plug-ins size, circularity, colour & fluorescent intensity included - PhenoSuite has a range of plug-ins for filtering colonies based on their size, circularity, colour & fluorescence. coordinates export - PhenoSuite automatically exports the coordinates of selected colonies to the ROTOR/Stinger platform for colony picking. Colour Upgrade available Upgrade available Fluorescent Intensity Upgrade available Upgrade available Coordinates Export Plate Normalisation Gene Mapping Control vs. Experiment Comparison (in replicate) Heat Map Visualisation

7 Y2H Package SGA Package Yeast 2-Hybrid screens allow you to examine every possible protein interaction in a pair-wise fashion. Identifying real interactions is tedious. PhenoSuite overcomes the bottleneck by automating the entire Y2H analysis workflow from colour measurement to data visualisation. Parameters can be fine-tuned and results can be exported so that you are fully aware and in charge of what has happened during each step of the analysis. In a genome-wide SGA screen it can be difficult to identify positive interactions because there are thousands of unique colonies in a screen. PhenoSuite overcomes the bottleneck of hit identification by automating the entire SGA analysis workflow from size and circularity measurement to data visualisation. Parameters can be fine-tuned and results can be exported so that you are fully aware and in charge of what has happened during each step of the analysis. Plug-ins Colour, circularity and fluorescent intensity - included PhenoSuite accurately identifies the colony colour and measures its circularity and fluorescent intensity. Plate normalisation - PhenoSuite takes into account external factors that affect colony growth and applies algorithms to normalise growth data so you can safely compare the data between plates. PhenoSuite currently normalises Edge Effect and Batch Effect. Gene mapping - PhenoSuite contains a database of strain locations for the most commonly used deletion and overexpression libraries, giving you the gene name of a colony by mousing over it. If you use custom libraries, you will have an option to upload a custom file for strain locations of that library. Control vs. experiment comparison (in replicate) - PhenoSuite automatically aggregates data from technical replicates and compares the data in the experimental plates against those in the control plates. Heat map visualisation - PhenoSuite presents the growth difference of all strains on a plate as a heat map, which allows you to quickly identify strains that have shown positive interactions in the screen. Plug-ins size and circularity - PhenoSuite accurately included measures the size and circularity of a colony. Plate normalisation - PhenoSuite takes into account external factors that affect colony growth and applies algorithms to normalise growth (size) data so you can safely compare the data between plates. PhenoSuite currently normalises Edge Effect and Batch Effect. Gene mapping - PhenoSuite contains strain location databases for commonly used deletion and overexpression libraries. If you use custom libraries, you will have an option to upload a custom file for the strain locations of that library, giving you the gene name of a colony by simply mousing over it. Control vs. experiment comparison (in replicate) - PhenoSuite automatically aggregates data from technical replicates and compares the data from the experimental plates against those from the control plates. Heat map visualisation - PhenoSuite presents the growth difference of all strains on a plate as a heat map, which allows you to quickly identify strains that have statistically significant growth differences in your experimental and control conditions. Upgrades Available Colour and fluorescence - If necessary, you can use colour and fluorescence as your read-out for your SGA analysis.

8 Random Mutagenesis Package Random mutagenesis screening is a powerful methodology for isolating strains with desirable phenotypes from genetically diverse populations. The ROTOR HDA and the Stinger can automate colony picking using the ROTOR/ Stinger, read more here. When it comes to data analysis, PhenoSuite then offers a complete solution from phenotypic identification to data visualisation. Plug-ins Colour, circularity and fluorescent intensity - included PhenoSuite accurately identifies the colony colour and measures its circularity and fluorescent intensity. Plate normalisation - PhenoSuite takes into account external factors that affect colony growth and applies algorithms to normalise growth data so you can safely compare the data between plates. PhenoSuite currently normalises Edge Effect and Batch Effect. Control vs. experiment comparison (in replicate) - PhenoSuite automatically aggregates data from technical replicates and compares the data in the experimental plates against those in the control plates. Heat map visualisation - PhenoSuite presents the growth difference of all strains on a plate as a heat map, which allows you to quickly identify strains that have shown positive interactions in the screen. About us For over eighty years, Singer Instruments have been designing and manufacturing cutting-edge scientific research equipment. No one understands the needs of microbiology researchers and yeast and bacteria manipulation better than Singers. From the automation of tetrad dissection using the MSM 400, the pouring of ultraflat plates using the Serial Filler, to the ROTOR HDA personal omics robot, no one has done more to make microbiology accessible to all. From its headquarters in the beautiful Exmoor National Park in Somerset, UK, Singer ships robotic systems and associated products internationally. World-leaders in instrumentation for yeast and bacteria, Singer Instruments are working hard to make continual improvements to help assist the scientific community.

9 Technical specifications Standard hardware set-up Support Standard Software set-up Plug-in Upgrades Model PhenoBooth Product name PhenoSupport Product name PhenoSuite Licence Model PhenoSuite circularity & filter plug-in PHS-202 product code PHB year product code SPB year Product code PSL-101 product code PHS-001 colour & filter plug-in PHS-203 Technical Specs Footprint: Width: 305mm Length: 305mm Height: 316mm Weight: 16kg Power: VAC Hz Max Power Consumption: 65w Camera specifications Scientific grade, HD CMOS Auto focus lens Warranty 1 year 3 year product code SPB year Product code PSL year Product code PSL-105 Hardware / Software Requirements Intel Core i5 2.4GHz 4GB of RAM 512GB hard disk space Windows 7 (64 bit), Windows 8 (64 bit) USB 3.0 port Licences 3 user licences for 1 year (all 3 licenses start from the date of first activation) Software Package Counting Package Software Packages Picking Package PHS-102 SGA Package PHS-103 fluorescent intensity filter Plug-in PHS-201 picking export plug-in PHS mm petri plug-in PHS-302 Plate Normalisation plug-in PHS-303 Gene Mapping plug-in PHS-304 Array Control vs. Experiment Comparison (in replicate) plug-in PHS-307 Heat map visualisation plug-in PHS-311 Y2H Package PHS-104 Random Mutagenesis Package PHS-104 Get a quote All information is correct at the time of printing. Some revisions may be made as specifications are improved. For more information please contact: sales@

10 Roadwater, Watchet, Somerset. TA23 0RE +44 (0) (tel) +44 (0) (fax) Get a quote Our distributors For a list of our distributors visit: /our-friends v1.4