User:WorkExp2017
Week 1
Monday
Wiki Reference Card: Wiki PDF
My assigned project for Monday was to name and categorize image files of embryo's onto an excel spreadsheet while listing any duplication of the files and images. These images include highly detailed photographs of the original embryo slides. The slides where taken from a donated embryo which was then preserved and sectioned a few microns each, which was then placed on slides. The digitized version of these slides are numerous and are quite sought after and posses a substantial amount of scientific value.
- In order to copy image file names onto an Excel spread sheet you must first open the command prompt then edit the selected drive to match the current drive the hard drive is located.
- This done by adding; d: to C:/Users/Unsw.Unsw-23098 then pressing the enter key. This will for example change the drive location to drive d.
- Then proceed to type dir which will give you the directory view.
- You then must find the folder that contains the file names you wish to copy then type cd (change directory) then the file name.
- Press the enter key and then type once again dir which will bring up the list of all the file names in the selected folder.
- Type dir then space > then create a name for the new filenew file.txtwhich will transfer all the names into a text file.
- Finally open up the folder location and open the text file then select delimited, tab, space options then enter. after auto fitting the excel spreadsheet should have the entire list of names. For small amounts of folders just right click, rename then copy and paste.
This link depicts each step taken. [1]
The majority of hard drives where categorized on an excel spreadsheet and i began to identify duplicate folders on a separate spreadsheet. Folders from the hard drives containing the images have had some files and even hard drives completely duplicated and it is imperative they are located.
Tuesday
On Tuesday i had identified all the duplicates and had listed them on the Excel spreadsheet. I then was tasked with uploading the images to the OMERO database. Dr Mark Hill (my employer and supervisor) taught me how to up load these slides as well as how to identify compressed files and non compressed files to upload. After realizing the extent of non uploaded slide i began immediately. After being given temporarily administrative privileges i began to upload the files and fill the many blanks that where missing in the database. I was also warned that there are some slides that refuse to upload and i was instructed to list those that where failed or avoided on the Spreadsheet. This procees due to the sheer size and amount of the images will take up a large portion of my work experience time and it is vital that the task is complete before Dr Hill travels to Berlin to discuss the issues and overall concepts of the extensive collection. The steps for uploading the slides are as follows:
- Login to your OMERO web-client and go to your desired group. (e.g Heinrich)
- Login to the OMERO software and select import data.
- Choose the drive that data is being uploaded from and select which files/slides you wish to upload.
- Reference the OMERO Web client to view which slides are missing form the Data base
- Now name the new folder, select where it must go and queue your request. Rinse and repeat.
- Example - Blechschmidt 1950 04 20 Slide 2 - 32
Online Database - Uploaded 62 slides
Wednesday
Wednesday I attended a morning seminar about Uveitis, an autoimmune inflammation of the eye. T cells produced in the thymus and are responsible for attacking diseases, specifically with Uveitis, in the eye in which the target foreign bodies to fight off infection. They however will enter the interior of the eye to fight of infection and the Alpha-Beta T cells will react with antibodies in the eye causing inflammation. Cataracts, glaucoma and others may be a side effect of Uveitis. Cortical steroids are an effect treatment though there is a high chance of the Uveitis repairing.
Why do autoimmune diseases relapse?
Prof Gerhild Wildner (Ludwig-Maximilians University, Munich)
Section of Immunobiology, Dept. of Ophthalmology, Ludwig-Maximilians-University, Mathildenstr. 8, 80336 Munich, Germany. Gerhild.Wildner@med.uni-muenchen.de
After the Seminar and morning tea i continued the uploading of the slides to the online data base.
Online Database - Uploaded 262 files
Thursday
On Thursday I continued with the uploading the files on to the database using the OMERO program. I as done previously, I continued to tag each embryo with which collection it belongs to, the embryo's CRL and the plane of cut the embryo was spliced and photographed. Though the program with the recent update has improved many key errors in the OMERO software, the program can still use improvements. For example, collection owners and viewers alike cannot properly view the large majority of images if the file contains large amounts of slides. As the folders are to far below and cannot be selected, it would be wise to implement a scroll on the left side of the site which would allow users to effortlessly scroll through the many slides that file may contain. Anouther necessary change is the in software OMERO program specifically when importing files. After naming a slide or a file the obvious progression (e.g.: 001-002) will not be recognized or assumed by the software. As a result the owners must upload and name each slide manually which is as laborious as it is tedious.
Online Database - Uploaded ?? files
Friday
On Friday I was extremely fortunate in being given the opportunity to observe routine lab work being taken place in the School of Women's & Children's Health department. It was there Dr Dulama Richani gave me an induction into the lab, equipment, staff and purpose. She then introduced me to David who was the Dr who I was going to observe. After wards I then attended a Symposium on IVF and though I had some difficulty with the terminology Dr Dulama kept me informed during the symposium. After it was compete I then went to my work place and continued up till I was messaged to meet David in the labs. After donning the appropriate lab apparel I was tasked with observing David....
Post-Doctoral Research Associate | School of Women's & Children's Health | University of New South Wales
