19 September 2022

Things you need to know about figure-making for final publishing 12-1pm 19 Sept 2022

You may not know that often researchers process images incorrectly after collecting your original microscopy images, this is quite common when it comes to figure-making for publication. You are invited to join this Zoom seminar to go through the steps from original images to final publication.

When: 12-1pm 19 sept 2022 (Mon) followed with lunch

Where: Conference room L2 WIMR

Registration link: https://www.eventbrite.com/e/409705629567

30 September 2021

Zoom seminar: things you need to know about figure-making for final publishing 11am-12pm 30 Sept 2021

You may not know that often researchers process images incorrectly after collecting your original microscopy images, this is quite common when it comes to figure-making for publication. You are invited to join this Zoom seminar to go through the steps from original images to final publication.

Seminar time: 11am-12pm 30 sept 2021 (Thu)

Zoom seminar link: https://uni-sydney.zoom.us/j/84985690614

Zoom ID: 84985690614

7-9 September 2021

Agenda and Registration: Olympus Organoid Conference | Olympus LS (olympus-lifescience.com)

See Flyer here.

19 August 2021 Access to Huygens 21.04 from any computer

SVI have released a new licensing framework this year! This means you will no longer require an on-campus IP address to utilise the university license.

A step-by-step instruction is attached for you to access to the latest version Huygens 21.04. Feel free to contact me if you have any issues.

23 April 2021 1st Westmead Imaging User Group meeting

This year, we are going to create a platform, the “Westmead Imaging User Group Meeting”, for our users to communicate and share imaging/EM experiences/expertise/tips/tricks.

The user group meetings consist of a 30-min presentation about a research project/topic followed by a 30-min session for Q&As as well as open discussions about researchers’ image acquisition & data analysis concerns.

1^st Imaging User Group Meeting

When: 11am 23rd April (next Fri)

Where: Level 2 Conference Room WIMR & Zoom (online)

Talk:  “Seeing into a new dimension - using imaging to reveal the complexities of brain-microenvironment modelling” by Amy Sarker

How to attend: click the link below to register and make a choice about in-person or offsite Zoom attendance: https://www.eventbrite.com.au/e/westmead-imaging-user-group-meeting-april-2021-tickets-150850888067   

The schedule for 2021 is included below

11 Mar 2021 40X silicone oil lens is installed back on the Olympus Confocal replacing the trial 40X objective from 11 Mar 2021

After a year trial of Olympus’s latest high-end 40X lens on the Olympus confocal, we are now returning the trial 40X oil lens and replacing it with our previous 40X silicone oil from today (11 Mar 2021).  Please be reminded of the following important notes on the 40X silicone oil objective by clicking the below link.

Important notes on the 40X silicone oil lens

11 Mar 2021  trial of 30X silicone lens offered by Olympus (from 6 Aug 2020) is over from 11 Mar 2021

The trial 30X silicone objective has now been replaced with previous 10 X dry objective on the Olympus confocal and therefore no longer available. Users imaging thick tissue or live samples are recommended to use the current 40X silicone oil objective instead.

Zoom seminar: things you need to know about figure-making for final publishing 12-1pm 18 Sept 2020

You may not know that often researchers process images incorrectly after collecting your original microscopy images, this is quite common when it comes to figure-making for publication. You are invited to join this Zoom seminar to go through the steps from original images to final publication.

Seminar time: 12-1pm 18 sept 2020 (Fri)

Zoom seminar link: https://uni-sydney.zoom.us/j/97053713493

Zoom ID: 97053713493

A trial 30X silicone lens is available on the Olympus confocal from 6 Aug 2020

The current 10 X dry objective on the Olympus confocal has been TEMPORARILY replaced with a new 30x silicone oil one. This 30x lens is a trial offer by Olympus and it is great for imaging deep or live samples. Click here to access the instruction on how to use it.

Important notes:

1. You MUST use silicone oil (green bottle) rather than normal immersion oil (blue bottle) when use this objective.
2. The silicone lens is a very expensive (cost over 16k) and therefore I am calling for extra care when try it out.

This new silicone objective will offer excellent resolution (high NA 1.05), brightness, depth and it is recommended for imaging thick/deep samples particularly for tissue or live samples.

Imaging and Histology workshop 23rd July 2020 

• Image analysis using cellSens & whole slide imaging with the Olympus VS 120 
• Histology project 101

Westmead researchers are invited to the above combined Workshop organised by imaging and histology facilities scheduled on 23rd July 2020 in the C2.22 Conference Room WIMR (max 20 seats) alongside a concurrent online Zoom session.

Morning talks and afternoon hands-on sessions on cellSens software applications and Olympus VS 120 operations are available for booking via the links at the end of this email.

Morning tea and lunch will be provided.

About cellSens 

Our existing cellSens, installed on the analysis PC on level 2 WIMR (and Argus RDCs), is a general imaging analysis software available to the whole Westmead Imaging Community.

This easy-to-use program helps “count and measure” any microscopy images and is particularly powerful for larger sized images i.e. images acquired from the Olympus VS 120 slide scanner (VS 120).

Program

Morning: Seminars (Session 1, C2.22 WIMR)

Join one or more talks if you can, feel free to go when you have to 

• 00 -10.10 (10m) Welcome & introduction to the VS 120 (Hong Yu, WIMR)
• 10 -10.40 (30m) Histology project 101 (Virginia James, WIMR)
• 40-11.00 (20m) Morning tea + product display (Olympus Australia)
• 00-11.45 (45m) What can cellSens do for your imaging processing and analysis needs? (Sheng Le, Olympus Australia)
• 45-12.30 (45m) Everything about application of VS 120 and VS200 update (incl. deep learning module) (Hong Yu, Chunsong Yan & all users)

Afternoon: concurrent hands-on sessions 

cellSens software application (Sheng Le Olympus, C2.34 WIMR)

You are welcome to bring your data set for cellSens analysis

• 30-15.00 (1.5h) CellSens Training (Session 2)
• 00-16.30 (1.5h) CellSens Training (Session 3)

Olympus VS 120 optimal operation (Tong Wu & Chunsong Yan Olympus, J2.08 WIMR)

• 30-15.00 (1.5h) Instrument operation (Session 4)
• 00-16.30 (1.5h) Instrument operation (Session 5)

All you need to do

• RSVP by 20 July 2020 so we can plan catering

Adjustment to the data sync processing on the Olympus VS 120 

To minimise interference of data sync on image acquisition on the Olympus VS 120

From 1 June 2020, there is a minor adjustment to the data sync process for data acquired on the Olympus VS 120. In particular:

• the auto data transfer from the acquisition computer to the Scientific Platforms folder on the AD server won’t start syncing until you log off the acquisition computer (previously sync happened instantly).
• if you need data transfer to occur immediately, you can manually initialise sync process by clicking the “data-sync” icon on the desktop, this will sync straightaway with no delay. 

The original automated data management procedure remains unchanged ( https://sydneyuni.atlassian.net/wiki/spaces/WIF/pages/763887953/Data) and still applies to the Olympus VS 120 slide scanner: All data must be saved onto the local computer (kept for 7 days before auto deleting): F:\virtual slide images\”your_folder”. Your data gets transferred to the server automatically after you log off the acquisition computer: Scientific platforms (\\Scientific_Platforms\Cell Imaging\Olympus VS 120\”your_folder” (kept for 14 days before auto deleting). NO USB is allowed on the acquisition computer to minimize virus risk.

Remote access to imaging analysis software via ARGUS is now available

To better allow remote access to imaging analysis software we now are providing access via ARGUS.

• There are currently 3 high performance remote desktop computers (ARGUS) that can be utilised for imaging analysis.
• Argus 3 has additional software installed for imaging analysis.
• Imaging software including Huygens 19.10, Fiji, cellSens v2.1 (Argus 3) , Olyvia v3.1, cell profiler and others have been installed. CellSense and Olyvia will be temporarily available on Argus 3 until review on the 3^rd of June.
• To access these platforms please see the attached email and respond with an “I agree” indicating you have read and agree to usage terms. Please include your unikey for provision of access.
• Remote desktop software from outside of WIMR (Teamviewer & Anydesk) is not permitted on the physical analysis PC’s located in the data analysis lab. These are not supported @ by WIMR and can result in breaches of privacy if accessed when another user is logged on. For this reason, Teamviewer & Anydesk have been REMOVED from the physical analysis PC’s located in the data analysis lab.

Advantages to use Argus:

• You can take advantage of the Argus HPC (refer to the attached email for the specifications)
• Good for working from home
• Currently no fees are charged to access the software / hardware on Argus

Remote technical support is now available on imaging instrument issues via Zoom meeting 

Dear microscope users particularly those using Olympus Confocal, Olympus VS 120 and Nanozoomer,

Due to the current COVID19 pandemic, I partially work from home but I can still provide remote technical support/trouble shooting via Zoom meeting even when I am not on site. Zoom meeting allows you and myself sharing your screen which can help address your issues in an efficient way. If you are not familiar with Zoom, please visit here to get more info and hopefully you can sign up and become a Zoom user:  https://zoom.us/.

I have installed Zoom on the above 3 systems which are top 3 frequently used systems at the Cell Imaging Facility. When it comes to how to have a Zoom video meeting, it is generally straight forward if you access to the Zoom program installed on the microscope computers except Olympus VS 120. This is because the computer that runs Olympus Vs 120 is blocked for internet connection. Thus, I have attached a step-by-step instruction here for Olympus VS 120 users.

My Zoom ID is 505-919-1026. Look forward to helping out with your image acquisition issues via Zoom meeting. If you need to speak with me, feel free to call 8627 3211 from the lab phone, I will receive the forwarded calls from the lab.

Any questions, feel free to ask.

Kind regards,

Hong

A live cell imaging system, called JuliBR Cell History Recorder, has been set up recently at the Westmead Imaging Facility (Level 2, WIMR) and it is ready to use.