Virtual Microscope

Image repository at the Wellcome Trust

David Male — Fri, 27 Jul 2012 10:16:01 +0000

Good news – The Wellcome Trust have agreed to act as the primary repository for the scanned images. We have had some discussion about where the images would be most likely to be discovered by users. The Wellcome Trust have a very large repository of biomedical images, and seemed the most likely place that people would search for this type of image. However, they have had nothing of this size before. After some discussions with their acquisition manager (Emily Doyle) and technical staff, it appears that they can handle the large size images that we have – up to 3Gbyte per image. The plan is to transfer the image set from hard disc, once the set is finalised. It will probably take several hours to make this data transfer.

Images and slide sets – progress so far

David Male — Wed, 16 May 2012 08:01:38 +0000

The imaging is now proceeding well – I have about 150 of the planned 280 images captured.
I am about 6 weeks behind my original schedule, but the project has developed into a bigger resource than originally envisaged.
Arrigo Capitanio has completed the breast set, and has nearly finished a set of kidney pathology.

Peter Mooney at MK Hospital has offered loan of 20 sections of skin and gut biopsies.
Angus McGregor has sets of liver and kidney pathology, and now has a colleague helping with the selection.
Douglas Gray and Vivian Rolfe found a selection of basic tissue sections which means that the original basic set will be about twice as large as planned.
I think we will end up with ~320 images in the collection.

As with all such projects, it is getting the material together that takes the time, especially when the collaborators are pressed for time with their own work being a higher priority. I think that all imaging should be finished by the end of July, so that August and September can be used to write the legends and add them to the sections.

OpenLearn units on Histology

David Male — Wed, 16 May 2012 07:47:43 +0000

I have written three course units, which will support the virtual microscope:
‘Introduction to Histology’, ‘Histology’ and ‘Histopathology’.
These units will be available on OpenLearn as soon as the editing is completed. Currently they are just illustrated OU-style course materials, intended for 1st or 2nd year undergraduates. However, as soon as the URL for the virtual microscope and the appropriate slide sets are ready, I will be adding extra screens with links, so that the written material and the on-line microscope will work together.

Presentation to Heads of Biological Sciences

David Male — Thu, 10 May 2012 14:35:27 +0000

I gave a presentation to a meeting of the Society of Biology for the Heads of University Biological Science departments.
The aim of my talk was to outline what could be done with virtual microscopes, and to highlight the forthcoming on-line resource.
It was interesting to hear that many of them would like to see slide sets for plant sciences, microbiology and envirionmental science.
None of these are planned within the current slide sets. But it would be relatively easy to add additional sets, if people already have the slides available.
Potentially a new contributor could visit the OU to do their imaging, and once the images are processed they could then add the legends by remote access.
Each slide set would require a small amount of funding to cover the academic and programming tiime (say £5K-£10k) for each, teaching unit that was produced -ie one set of 30 fully annotated slides and any associated teaching material.

Histology units via OpenLearn and OpenScience

David Male — Wed, 04 Apr 2012 09:54:47 +0000

I have had discussions with the unit that runs OpenLearn at the OU. They have agreed to fund the addition of 3 units from an OU work-based course onto OpenLearn. The units are Introduction to Histology, Histology and Histopathology. I wrote these units originally, but because they were designed for work-based learning, and to be used with a digital microscope on DVD, and because they are currently pdf files, they require a lot of academic editing, and file conversion to make them suitable for on-line delivery.

The plan is to place the written units in OpenLearn, because that is the most suitable place for them, and to place the digital microscope within the OpenScience laboratory, because that will give it maximum exposure. By making links between the digital microscope and the on-line teaching material, the whole package should work transparently together.

The OU has recently received a £1m grant from the Wolfson foundation to develop the OpenScience laboratory, and the histology and geology virtual microscopes will be among the first elements to be presented within the laboratory.

Supporting Hospital Laboratories

David Male — Wed, 07 Mar 2012 15:10:38 +0000

I spent an hour with Peter Mooney at MK Hospital discussing what sections would be most useful for biomedical scientists who prepare such sections. Our current plans include a preponderance of pm pathology tissues, but they tend to see biopsies, particularly skin, lymph nodes and gynaecological tissue. I have asked whether the laboratory at MK hospital would be able to supplement to the collection in these areas, and they appeared positive.
Any thoughts on which tissues/diseases are most useful for this group of scientists, would be welcome.

Supporting GCSE and A-level studies

David Male — Tue, 28 Feb 2012 10:11:05 +0000

I have been talking to schools about how the digital microscope can support their students.
(Particular thanks to Andy Squires at Denbigh school for his help)
I have a list of sections that would be useful, including basic histology, some diseases and parasites.
A few items that they would like, but which were not included in our original plans are:
Basic cell structure, sperm and testis squashes, pituitary.
They particularly aim to teach structure-function relationships, but I think the material that they want can be accommodated within the basic histology sets, with pointers to the few specialist pathology slides they might use. Interestingly, the level of the legends that we already have on the slides (intended for level-2 undergraduates) is exactly what would be needed for A-level.
The one area that the schools would like and we have not got is plant structures. Although there are no plans to include this area it would be relatively easy to add a few slides, and we have the offer of a loan of slides from a local school.

Images format and new software

David Male — Tue, 21 Feb 2012 09:08:23 +0000

We have now installed ‘Surveyor’ with Turboscan on the microscope, which will allow us to tile much larger images. At the OU, we are aiming at images of up to 1Gigabyte, made from up to 300 individual images, using the x10 objective. At UCLH, Arrigo has been making images of up to 2.7Gigabytes using the x20 objective and 900 individual images, which gives excellent resolution and coverage of the section.

22-Feb update. We have now confirmed that the large tiff images can be handled within the virtual microscope. The conversion for the microscope takes about 10 minutes of processing with ‘zoomify’ for each image and produces a set of files that occupy ~200megabytes. If we produce 250 images, it will occupy 250 gigabytes in the image repository (larger than Jorum can accommodate) and ~50 gigabytes in the server of the virtual microscope.

David Male — Thu, 09 Feb 2012 10:51:24 +0000

Angus Mcgregor, (Consultant pathologist) is in touch with Douglas, and says that he can contribute sections on liver pathology which is his specialist area and possibly also some kidney sections.

Image capture system upgraded on the real microscope

David Male — Tue, 07 Feb 2012 10:48:16 +0000

The microscope which we use to take the scans has been upgraded (Jan 31st), with the addition of a new camera, computer and software, which will allow us to take larger images (up to 1 Gigabyte). The software also improves the tiling of the individual frames, by compensating for any inaccuracy in the alignment of the stage and camera.