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Tip

Learn more about clearing methods:

  1. If it's the first time, you can start by reading the following paper: Ariel, P. (2017). A beginner’s beginner's guide to tissue clearing. The international journal of biochemistry & cell biology, 84, 35-39.

  2. The table that compares different methods: Richardson, D. S., & Lichtman, J. W. (2017). SnapShot: tissue clearing. Cell, 171(2), 496-496.

  3. Water-based clearing protocols (such as CLARITY/SWITCH), can be done in the unit , using the LifeCanvas SmartClear II.‏

  4. iDISCO method

  5. PEGASOS method

Frequently Asked Questions:

  • How do I save and access my data?

At the end of the experiment, save the data in the “SWAP "SWAP (z:)” " driver.

Once the data is synchronized in the sever, connect to one of the following workstations: Bali/Maldives/Bahamas (20T_2/ 30T/ 20T).

On the workstation desktop, find and click on the script “map SWAP“"map SWAP ".

Next, transfer your data from SWAP to the gpfs0(G) disk (ESS) in the following manner:

Open driver G.

Go to the “Labs” "Labs" folder, open the folder of your PI, open a folder with your Weizmann user name.

Copy data from SWAP to the “Raw"Raw_Data” Data" folder.

Before you delete the data from SWAP, make sure that the data is fully copied and opens in the relevant analysis software. Also, note that only the “Raw"Raw_Data” Data" and “Analyzed"Analyzed_Data” 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. 

stitching

  • 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?

  1. Mark to the "Multiview" box.

  2. Chose 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.

  3. save it

  4. open "light-sheet tile scan (on the bottom near the zen icon.

  5. load the file

  6. bounding box

  7. mark change +10% overlap

  8. image size-save

  9. back to zen

  10. remove points

  11. load the file

Info

Suitable for live (morphogenesis/embryogenesis, 3D culturscultures/ 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

  1. Multiview imaging for maximal 3D resolution, multiposition imaging

  2. Combines environmental control for prolonging imaging with minimal perturbation

  3. Emission filter combinations covering fluorophores excited by the 405-633

  4. CCD at 16it

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