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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. 
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.
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.
Online Database - Uploaded 62 slides
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
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 they may find laborious and/or tedious.
Online Database - Uploaded ?? files
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 extracting the granulosa cells from the blood cells. After the containers where ascertained, David first got rid of the clots in the blood then extracted the samples using an anti clumping solution from the container and through a filter. This filter had Small enough that blood cells could pass through but not granulosa cells. This technique is most effective when there is large amounts of granulosa cells. He then using granulosa to ensure the cells did not clump together, placed the cells on petri dish in which he then conducted a cell count. The cells where placed in a test tube in which they where run through a centrifuge to seperate an place the cells at the bottom. The end product was a test tube with very little granuloas cells ( roughly 24 000 ) and the majority being blood cells . The cells where the n placed in to the freezer for later use and experimentation. Though the results slightly disappointed David, i still feel gratified of being allowed the opportunity to experience a lab environment thanks to the efforts of David, Dr Dulama and Dr Mark Hill.
Post-Doctoral Research Associate | School of Women's & Children's Health | University of New South Wales
I began uploading files to the Bochem collection which i began to realize doing so would be far more difficult to do. To begin with, not all the files are compressed unlike in the Gottingham files which all are. This essentially means that a large majority of the files are not permitted to be uploaded to the Database resulting in some cases a whole embryo or embryo slides missing entirely. Another daunting issue with the Bochem drives is that not all of them are formatted correctly into the jpeg. As a result i must hand pick and choose which files are and aren't in a collection as the software will fail to upload any slides that aren't formatted properly. Another issue that is is situational and occurs at random is that if a batch has finished uploading and there is no other uploads waiting to be uploaded, uploading another batch will cause it continually pend and it will not scan or progress forward at all. This however seems to dissipate as it happens occasionally or in some instances many times in a row. The only solution is to completely close the software and reboot it every time this error occurs. Despite this i had the pleasure of participating in an engaging lecture presented by my employer Dr Mark Hill. The premed topic was cell biology and primarily focused on cell membrane structure and purpose. The cholesterol/sugars, lipids and the proteins located in the cell membrane where discussed in detail as well clips of cell structure and movement. It was an interesting lecture which i had far less difficulty following as it shaped around a year 12 biology as some of the students hadn't done biology prior to entering UNSW,
I attended a premed cell biology lecture with my employer being the lecturer. The lecture was a continuation of the Mondays lecture but focused more heavily on the Cyto skeleton and plasma of cells. White blood cells where commonly referenced. Before the lecture i was tasked with continuing updating the Hiendrichson collection. This as usual was the bulk of my task work while updating the DEC spreadsheet about the files.
Wednesday was the day that all the Hindrichson files had been uploaded onto the database and so it enables to focus all my efforts on completing the Gottingham collection. Mark has suggested that due the large amount of slides and the limited time, it would be wise that when it comes to Embryo's with large amounts of slides, it would be best if i do every 10th or 20th which he has left to my discretion. Mark also offered to to buy me lunch which i happily accepted and while talking we discovered we had a mutual interest in Star Trek. Afterwards i continued uploading till the end of the day.
As Dr Mark is leaving at 3:00pm tomorrow, my task was to allocate and separate which entire hard drives had copies of all its embryos else where and could be wiped so that mark in Berlin can upload more embryos onto the hard drives to be later uploaded onto the database. This task essentially looking at all the files in a drive, see if they are in 05 (the drive i believe to have almost all embryos) or 09 and if they are present in those drives, i am to stack them in a separate pile form those hard drives that have embryos that can only be found on a single drive which Dr Mark is going to keep.
Today is my final day at the Wallace Wurth SOMS and it was a rare privilege to be able to work in such a immaculate, friendly and professional environment. On my final day i have double checked the drives mark is taking to be wiped are present on other drives. I have also updated the spreadsheet and attended a morning lecture on the structure and function of cell biology. I leaned about how by looking into the cyto plasma can you see the organelles and the membrane structures . Learning about Ribosomes and how they create protein when the RNA sequences are covered into amino acids. As a result, i the lecture also included the Endoplasmic Recticulum which is an organelle and is located in the cytoplasmic space. Smooth Endoplastic Recticulum have no Ribosmes attached and their function is to detoxicate drugs and harmful compounds out of the system, carbohydrate and lipid metabolism. Rough Endoplasimic Recticlum is resposible for changing and directing proteins to specfic destinations . It s is also in charge of exports from the cell. While the some of the lecture was hard to grasp as i am as of this year still a year 10 student, a lot of the concepts i have manged to wrap my head around such as the three main componnents in the membrane; carbohydrates ,protein and lipids. Though i find structure easier to understand than function as a lot of the terminolgy during lectures is foregin to me, i still am picking up a lot just by listing and is a testament to Dr Mark Hill's teaching ability.
As mentioned prior, i am truly grateful for being accepted into the work experience program and i do hope in a few years time i arrive at here at SOMS not as a work experience student, but a student in medicine.