Big Image User

[saloynton]

Introduction to Clinical Pathologist 25/11/10
Background notes of Joanne's work

Joanne is at a preliminary phase in her research where she is still outlining some of the remaining plans and where the full scope of questions for the work lies. Her research work her work is specifically following on from findings that have been made in Lloyd’s laboratory.

She is working with several of the technicians at Ninewells hospital who will be helping her preparing her tissue work. One of the other reasons she is working with Ninewells is the main constraint she is working under is the clinical machines that would be used for such clinical pathology work, are not available at Dundee.

The background to the workflow of clinical pathology is that they have traditionally not working with digital data because of the scale of the images. This has meant the scientists are quite happy to work with their slides and continue to use microscopes and have a physical interaction with their work. Joanne was an example of this in how she would find it very strange in not having to look down a microscope, she has been part of group meetings where the team will analyse images and her colleagues find the transition of viewing digital data bizarre and have a preference to being able to have control with a physical slide.
Some of the other noted difference between the practices in fluorescent microscopy and the practices in clinical pathology is the staining of images. In clinical pathology this is restricted to 1-2 colours the pathologies are also typically able to work at a lower level of magnification because they are not using oil to view the tissue.

One of the existing tools Joanne was using was the human protein atlas. (​http://www.proteinatlas.org). This tool has been add to the review of existing big image viewer tools see ticket #3573.

The follow up work and contact with Joanne is to help gather some background of her workflow but this may have some restrictions on gathering actual image data. The follow up time has not yet been determined as Joanne is waiting on the next phase of work to be determined and completed. I will need to contact her the week beginning 13th Dec to confirm when the meeting might take place.

UPDATED - Meeting 14th Dec

Joanne is currently progressing with her research she is due to receive the cell cultures in order to continue her work. She has begun to view several of the newly imaged slides that she has received. Her next phase of work is in the analysis of the images and the identification of the brown spots. Her ideal tool for this is a cell counter that may distinguish and clearly identify the brown spot.
The tool she will be using for this is ImageJ. It was discussed the ability to work with OMERO and ImageJ so there might be some potential to explore the workflow between ImageJ and Insight if required. (Access to some sample images are available)
The next few months of her work will be subject to the outcomes of the results of the anti-body and if the quality of the results will require further analysis.
As the big image work progresses Joanne will need to further updated and so that we may stay up to date. Action contact again week beginning 7th feb 2011 for OMERO update.

UPDATED: To contact the week beginning 25th April for to confirm the position of her work. It will need to be addressed how much further along she is with her work as she would be a suitable candidate to preview/demo/test some of the big image work. From the previous meetings this might be problematic as her workflow has not been completely through the use of digital images.
The schedule will be required to demo when available OMERO with big images is to use this as a the proposal for her new workflow.

From the initial meetings part of this integration will be dependent on the use of ImageJ for spot analysis.

[jburel]

Moved from sprint 2011-05-05 (11)

[saloynton]

Current status: I have only been able to speak with her briefly to let her know I was planning to see her. And when I have visited the lab she has not been, around so I am still waiting to meet with her.

[saloynton]

I have spoken with her today (10th May). Her work is still waiting on various aspects so she is still some time away for her to be more
focused on the imaging part of her work. ' I have proposed that a version will be available for her to use within 2-3 weeks. She is very happy to see
this so it would make her a candidate for being able to test the viewer.
However, because she is not in the imaging phase of her work, she will not be able to test the big image viewer in 'anger' so any possible
testing would be minimal.

The ticket will remain open as the preview/testing with the user is arranged.

[jburel]

Moved from sprint 2011-06-02 (13)

[jburel]

Moved from sprint 2011-06-16 (14)

[saloynton]

I have had a problem viewing her images the tiff is not clear at all. I have attached a screenshot.

[saloynton]

Chris just to confirm the image imported into imageJ as expected with the latest version of bio-formats.

[saloynton]

The subsequent ticket of #6124 has been created to investigate the problem with the image.

[saloynton]

Closing ticket the user was no longer required for scoping the big image work.