Learn more about Light Sheet microscopy:
Richardson, D. S., & Lichtman, J. W. (2015). Clarifying tissue clearing. Cell, 162(2), 246-257.
Learn more about clearing methods:
If it's the first time, you can start by reading the following paper: Ariel, P. (2017). A beginner's guide to tissue clearing. The international journal of biochemistry & cell biology, 84, 35-39.
The table compares different methods: Richardson, D. S., & Lichtman, J. W. (2017). SnapShot: tissue clearing. Cell, 171(2), 496-496.
Water-based clearing protocols (such as CLARITY/SWITCH), can be done in the unit using the LifeCanvas SmartClear II.
Frequently Asked Questions:
How do I save and access my data?
At the end of the experiment, save the data in the "SWAP (z:)" driver.
Once the data is synchronized in the sever, you have 2 options:
1- On the computer next to LLS, login with your weizmann user. Next, tansfer your data from SWAP folder to the gpfs0(G) disk (ESS) in the following manner:
Open driver G.
Go to the "Labs" folder, open the folder of your PI, open a folder with your Weizmann user name.
Copy data from SWAP to the "Raw_Data" folder.
2- Connect to one of the workstations.
On the workstation desktop, find and click on the script "map network drives".
Next, transfer your data from SWAP to the gpfs0(G) disk (ESS) in the following manner:
Open driver G. Go to the "Labs" folder, open the folder of your PI, open a folder with your Weizmann user name. Copy data from SWAP to the "Raw_Data" folder.
Before you delete the data from SWAP, make sure that the data is entirely copied and opens in the relevant analysis software. Also, note that only the "Raw_Data" and "Analyzed_Data" folders are backed up.
Please note that only data acquired on the Lightsheet microscopes can be stored on the gpfs disk (ESS). No other data is allowed on this gpfs disk !!!
For Data organization on the ESS, please refer to ESS Guidelines.
How to stitch the data in "Imaris stitcher "?
1- First book the following in the internal services:
One of the following workstations: Bali/Maldives/Bahamas (20T_2/ 30T/ 20T)
Software license for: Imaris and Imaris Sticher
2- On the work station, transfer your data from SWAP to the gpfs0(G) disk (ESS)
3- If needed, do "dual side fuse" in zen black.
4- Open Imaris converter, convert the data to Imaris format
5- Open Imaris stitcher and add the converted data
6- More info can be found in Imaris Stitcher Tutorial.
How to do tiles in the light sheet microscope?
Mark to the "Multiview" box.
Check the image size and set the right one.
In the "MULTIVIEW" window that has opened, add two (or more) points on the edges of your sample. Note that the z stack is the same for all tiles. Make sure that it covers the whole structure.
Save the file on the desktop.
Open "light-sheet tile scan" (icon- the screen bottom near the zen icon).
Load the file that you saved.
Set to 10% overlap.
Insert the correct image size.
Click "Bounding box".
Save- rewrite the file.
Go back to zen.
Remove the points in the "Multiview" box.
Load the file.
Start the experiment.
Suitable for live (morphogenesis/embryogenesis, 3D cultures/ spheroids) fixed, or water-based cleared (CLARITY/ Scale /Pact) whole tissues.
Objectives:
excitation:
5X and 10X
detection objectives:
Air: 5X
Water:10X-20X-40X
Clearing: 20X clearing for 1.45 Refractive index / 20X clearing for 1.38 Refractive index
Multiview imaging for maximal 3D resolution, multiposition imaging
Combines environmental control for prolonging imaging with minimal perturbation
Emission filter combinations covering fluorophores excited by the 405-633
CCD at 16it
