Within the software IN Cell Analyzer:

1. Click Eject to open the access door
2. Insert your sample in the space provided for this purpose, respecting the orientation indicated

3. Click Load to close the access doors

   First use

   During the training you will follow the First use protocol

   Important

   For use with the 60x objective it is absolutely necessary to use a multi-well plate with a glass bottom. The glass thickness should be 0.17mm. We recommend the following plates:

1. Collect your samples
2. Click Load to close the access door
3. Close the INCell Analyzer software
4. Transfer your data to disk D: (Data Storage) or to your external hard drive and delete it from local disk C:
5. Turn off the computer

• Files can be saved temporarily (during acquisition) to local C: drive (desktop)
• At the end of each session, copy your data to your external drive and delete it from local C: drive
  
• You can store your files on the D: drive (Data Storage). If you do, please create one folder per laboratory using the principal investigator's last name. Inside, create a folder per user using the following nomenclature (First Name_Last Name).

When using the microscope for the first time, it is necessary to define the type of plate used. You will usually do this during the training session .This procedure can also be performed if you are using a different multi-well plate.

Create a new plate

In the INCell Analyzer software:

1. Select from the menu Application>Plate\Slide Manager...
2. Click on the New Plate\Slide icon
3. Select the number of wells in your plate (6, 24, 96 etc...)
4. Adjust the following settings:
   1. Name: Your-Name_Your-Plate
   2. Plate height, bottom thickness and well volume usually provided in the product technical sheet by the manufacturer
   3. The material used plastic or glass
   4. If necessary adjust the number of rows and columns as well as the shape of the well (round or rectangular)
5. Click OK
6. Close the Plate/Slide Manager window

Measure the bottom height and thickness of the plate bottom

In the INCell Analyzer software:

1. Click on the Dashboard
2. In Objective Lens select the 10x objective
3. On the plate plan, click on the center of a well containing a sample to center this well on the objective
4. In the Dashboard menu select Plate/Slide
5. Click Verify LAF
6. If the 2 detected peaks (blue vertical lines) correspond to the measured peaks (black curve)
   1. Click Apply Measured Parameters
   2. Click OK
   3. Click Yes
7. If the 2 detected peaks (blue vertical lines) do not correspond to the measured peaks (black curve)
   1. Change the bottom thickness value and repeat the operation
8. Close the Laser Autofocus Plate/Slide Verification window

Measure A1 well offset

In the INCell Analyzer software:

1. if necessary, click on the Dashboard > Objective Lens select the 10x objective
2. In the channel list, click the + button and add a transmitted light channel (brightfield)
3. To the right of the plate layout, click the Setup Preview Imaging button
4. Draw a rectangle around well A1
5. Click on preview (on the acquisition panel at the top right of the screen)
6. Wait for the preview to be generated
7. On the plate map, click on the real center of well A1 to center this well on the objective

8. In the Dashboard menu select Plate/Slide

9. Click Edit Plate then Define Upper Left Well

10. Click Yes

11. Check that the yellow circle matches the edges of the well

12. Click Yes

Compute the inter-well distance

• Repeat the offset measurement steps for the bottom right well

• The inter-well distance will then be automatically calculated

Because of an issue with the liquid handling motor, the liquid handling arm as been replaced by a standard fixed arm for the transmitted light LED. Therefore liquid handling is no longer available.

Y motor not resting when reaching the transmitted light position: This time the issue is slightly different: Y motor is homing properly during the initialization procedure but instead of resting it keeps pushing toward the home position and after a brief instant the instrument stops and the red light shows up. If the liquid handler Y motor is disabled the initialization proceed properly and the system is usable at the exception of the brightfield of course

• Added to wiki

Usually, this microscope displays a green light when operational and an orange light when in use. A red light is on means the microscope is not functional. In this case please contact the platform manager.

Usually the microscope remains on. However, it is best to turn it off if not in use for a long time (weeks). To do this:

1. Navigate to the menu Application > Hardware >
2. Click Shutdown Instrument
3. Wait for the microscope to turn off
4. The software closes automatically