Frequently Asked Questions
What if I don’t know exactly what I want to measure?
We can provide advice on the best approach for your image analysis based on our experience in the area. We routinely carry out image analysis algorithm optimisation work on pilot samples from our clients and then arrange an online meeting to discuss the details to allow changes to be made before proceeding with the analysis of the main study.
What if I only have histology slides and no images?
You can send your histology slides to us and we can convert them to digital images using our Hamamatsu Nanozoomer slide scanner. We can then carry out the analysis on the digital images and send the data and image back to you.
Can you analyse formalin fixed paraffin embedded tissue?
Yes. We can perform analysis on tissue that has been fixed using any established method. Good tissue quality is paramount and will effect both the Histology/IHC performed and subsequent image analysis.
Can you measure data across the whole section?
Yes, we use software which allows analysis across the whole tissue section or particular regions of interest within the tissue section, depending on the clients preference.
Can you provide quantification of the area of staining?
We can provide detailed analysis across any whole slide image or specific/specified region of interest within that tissue. This can be quantification for an area of marker staining or at a cellular level to deliver accurate cell-by-cell quantification of membrane, cytoplasm or nuclear staining.
Can you determine the number of positive and negative stained cells?
We can perform detailed quantitative analysis on a cell-by-cell basis across the whole slide image. Cells immunohistochemically stained with either a membrane, cytoplasmic or nuclear marker can be positively identified and quantified as individual cells or as an area measurement across the whole tissue section.
Can you quantify fluorescent labels?
Yes, we can quantify immunofluorescent labeled antibodies, either as single label IHC study or as part of an IHC multiplex study (allowing for colocalisation to 2 specific markers in the same tissue / cell). We can further use specific fluorescent labels to identify particular regions of interest in a tissue (for example Pan CK for tumor tissue) and then determine a target specifc label within the region of interest. For some examples of our fluorescence work please see our image analysis gallery.
Do you carry out co-localisation quantification?
Yes we can perform colocalisaton of markers in the same tissue. For colorimetric stained sections we can quantify the area of two markers (red and brown) plus the area of colocalised read and brown on the same section. For fluorescent stained sections, we can quantify the number of cells which are positive for either specific marker and the number of cells that are positive for both colocaliased markers.
What if I only have tissue slides and no images?
No Images, no problem! We can scan your slides using our Hamamatsu Nanozoomer and return the whole slide digital images to you via our secure cloud server and/or on a portable hard drive.
Can you analyse tissue multi arrays (TMAs)?
Yes, our software enables us to quantify parameters within TMA cores from both colorimetric and fluorescent stained slides. Each core is deteced as an individual tissue and marker staining quantified as an area or on a call by cell basis to give a postive cell count or Histological score (IHC intensity). We can also perform cell compartment analysis on TMA cores to quantify marker staining speicifically within the nucleus, cytoplasm or membrane of each cell. See the TMA example in Image Analysis Gallery for more details.
Can you analyse frozen tissue sections?
Yes. We can perform analysis on frozen tissue sections. Remembering that good tissue quality and slide storage is paramount and will effect both the Histology/IHC performed and subsequent image analysis.
Do OracleBio also provide Histology and IHC services?
Yes, OracleBio can supply quality non-GLP and GLP Histology / IHC services via our links with partner companies. For more details see the partner services section of our website.
What if I just want to scan my slides with no analysis?
No problem. We offer a slide scanning service using our Hamamatsu Nanozoomer slider scanner. Slides can be scanned at x20 or x40 magnification in bright field or fluorescence mode. For more details, see the Slide Scanning section of our website.
Can OracleBio supply a report with statistics?
Yes, we perform statistical analysis for many of our clients and all data will be included in the final report document. We are happy to perform analysis in a blinded fashion with specific statistical analysis being carried out once the data have been generated.
How much does it cost?
The cost of the image analysis is dependent on a number of factors including, size and complexity of the tissue, the number of parameters to be quantified and the amount of manual corrections required to remove artifacts etc. Please contact us and we would be happy to discuss your requirements and provide you with a quote for the work.
How long will it take to receive my data?
Turnaround time will depend on the total number of slides and markers to be analysed. For example, for 50 slides analysing a single marker on a whole tissue section, data would be returned to the client within 1-2 weeks of receiving the digital images. Data would be returned to the client as soon as the analysis and quality control was complete, release of a formal report of the data would take longer.
What type of image formats do you accept?
Our software works with most image formats (tiff, jpeg etc). Higher quality images, such as those produced by a digital scanner, will provide better quality data and we can work with whole slide images generated from a wide range of scanners including Aperio, Leica, Olympus, Hamamatsu, Mirax, 3D Histech etc.
I need a histological score measurement, do you do this?
Yes, we can provide histological score measurements in an objective and reproducible manner using our software. Each cell within a tissue can be individually detected and classified based on their marker IHC intensity as negative, positive low, positive medium or positive high. A histological sore is then generated on a scale of 0 – 300, representative of all the cells analysed in the whole tissue section or region of interest. Statistical analysis can be performed on tissue group means for interpretation of response.
Do you also provide Pathology review services?
Yes, we have strong links with clinical and CAP registered veterinary pathologists who can provide a review of your slides, selection/guidance of specific regions of interest for analysis and generateion data reports.
What would the final data package include?
The data package will include image analysis raw data files (csv), Excel data summary tables, image analysis screenshots (jpeg), original images and, if required, a detailed report.
Can you work on my clinical trial samples
Yes, we have worked on a number of clinical trials and are happy to work with you and/or your preferred CRO of interest to deliver your image analysis requirements.
Can you advise on the best approaches for carrying out quantitative IHC?
Yes, we have a number of years of experience in optimising IHC protocols, gained whilst working in the target validation departments of large pharma. We can advise on best practice for optimal storage, processing and staining of tissues to provide quality image analysis data.
Is there an easy way to transfer files and data to you?
Yes, OracleBio have a secure server which allows easy upload and download of images and data from your desktop computer. Contact us and we can provide you with login details to your own folder.
Can you also procure tissue?
Yes, we can procure specific tissues for your studies via our network of partner companies. See the Partner Services section of our website for more details
Can you project manage our histology, IHC and image analysis needs?
Would you be prepared to work with our current preferred CRO’s / Suppliers?
Yes, we work with a number of partner companies and would be happy to work alongside your preferred suppliers.