Axio Scan Z1

Axio Scan Z1 Operating Manual

1. Make sure the slide scanner switch on the back and on the frontPicture1.png

2. Login to the computer with your NETID and IGB password

3. Start ZEN blue then clicks on ZEN slidescanPicture2.png

4. Load your slides into the trays, place your slides face up with the label in between holder then press the silver button on the instrument or open using Zen. 

image-1654698722873.png

Note: occupied slots are highlighted on slide scanner in blue, green, orange, red or white.

5. Storage location: direct the folder to save your images in: D:\User Files Deleted Anytime Picture4.png

Note: After scanning, make sure you transfer your data to the core server under your PI’s NETID: \\core-server.igb.illinois.edu 

6. Mark All: All slides are displayed in the Magazine tab that appears automatically when slides are loaded into AxioScan.Z1. Unmark All slides to avoid compromising other experiments. Picture5.png

7. Select profile from default scan profile then click the gear icon to open advanced wizard and modify your settings Picture6.png

Setting Up Brightfield Scan Profile  

1. Global Data

BF1.png

  1. Label Scan Settings: This tab allows you to adjust the size of the window displayed in red that defines the slide label image size and position, the image always save in separated file called pt1.BF2.png
  2. Preview Scan Settings: the red rectangle defines the space on the slide that will be used to detect the edges of tissue detection. Note: Sometimes it is useful to reduce this area to improve the automatic tissue recognition on the slide borders, you might want to check if the predefined size corresponds to your needs. The image always saves in separated file called pt2.               BF3.png
  3. Tissue Detection Settings: check Automatic and use Test to check the quality of the recognition. The display curve (C) can be modified to change the contrast of the image (set as best fit) and help your eyes to see the tissue clearly. The yellow ROI shows where Zen will obtain data for the shading correction. Notes: Green ROIs are defined by the following parameters (see Application guide AxioScan.Z1 v1.1):

    4.A. Specimen histogram (A) can be modified to select specific intensity values (detail in fig below).

    4.B. Region dilation size (B) defines a value for spacing the border around the detected tissue.

BF4.png

FL.png

5. Focus Map Settings: Axio ascan Z1 uses a two-step focusing method (Coarse and Fine) to give the best results.

5.1. Coarse focus looks for tissue’s macroflatness, which basically means that tries to locate the section on the slide.

5.2 Fine focus looks for tissue’s microflatness which identify small focus within the section.

6. Scan Settings: Adjust the flash intensity or flash duration to get desire image for final set up.                                BF-scansetting.png                                      

Fluorescence Scan Profile

1. Global data: the profile type should be fluorescence, tissue detection mode is automatic, TD recognition type for fluorescence is marker. Channel is recommended mode for AF contrast type coarse or AF contrast type fine                                                      FL-1.png

Note AF Contrast Type Coarse and Fine are channel and RAC, only for fluorescence profile. 

2. Label Scan Setting                                                                                                                                                        FL-2.png                                                                                                                 

3. Preview Scan                                                  FL-3.png

4. Tissue detection settings: check automatic and test, if green ROI does not cover your tissue, you can adjust the histogram under marker (A), region of shrink size (B), adjust the histogram on the display to best fit to see the tissue clearly (C).    FL-4.png

5. Focus Map Settings: Axio scan Z1 uses a two-step focusing method (Coarse and Fine) to give the best result.

5.1. Coarse Focus

5.2. Fine Focus

6. Scan settings:

Tutorial videos on how to set up brightfield and fluorescence for Axio Scan Z1 by Zeiss can be found in this link https://www.zeiss.com/microscopy/us/local/zen-knowledge-base/axio-scan.html

 

 

 

 

 

 

 

 

 


Revision #5
Created 8 June 2022 14:14:37 by Ni Putu Dewi Nurmalasari
Updated 17 January 2024 17:16:29 by Ni Putu Dewi Nurmalasari