Instruments/Zeiss-Elyra-7.md

@@ -6,26 +6,29 @@
 
 ## Startup
 
-Zeiss Elyra 7 
-Start-up
-The Elyra microscope has only one switch that needs to be turned on. The first one is the Main Switch, which is a turn knob. Do not turn any other switches on/off. Next, you will need to switch on the computer under the table. If at any point during your experiment a loud peeping noise goes off, first check the CO2 sensor (and leave if noise if coming from the sensor). If not, the noise is coming from the cooling system behind the Elyra and you need to [refill the cooling liquid](Maintenance/Elyra 7#Cooling-System). 
+1. The Elyra microscope has only one switch that needs to be turned on (Main Switch), which is a turn knob. Do not turn any other switches on/off. Next, you will need to switch on the computer under the table. 
 
 ![Turn_on_Microscope](uploads/aac5d9df0740e27fa7c0b7e155e7545e/Turn_on_Microscope.PNG)
 
-Choose the correct objective you want to use for imaging (via the touch panel, menu point 'Microscope') and press 'Load position' to bring the objective down to its lowest position.
+2. If at any point during your experiment a loud beeping sound goes off, first check the CO2 sensor (and leave the room if the sound is coming from the sensor). If not, the noise is coming from the cooling system behind the Elyra and you need to [refill the cooling liquid](Maintenance/Elyra 7#Cooling-System). 
+
+3. Choose the correct objective you want to use for imaging (via the touch panel, menu point 'Microscope') and press 'Load position' to bring the objective down to its lowest position.
  
 ![PXL_20240320_100556693](uploads/d4ffa9faf03159d965836f375e6a8496/PXL_20240320_100556693.jpg){width=49%}  ![PXL_20240320_100603288](uploads/03d6e4050d79e349b342fbf4b9051f85/PXL_20240320_100603288.jpg){width=49%} 
 
-With the front window open and the light in the incubator on (switch to the left, on the microscope table) you can safely navigate larger distances when using the joystick (which has an inverse logic). 
+4. Start the 'Zen black' Software and press 'Start up System'
+5. The temperature inside the incubator will be by default at 27°C to minimize drift. Use the oil for 30°C. Immersion oil bottles for 30°C and 37°C are stored in the incubator at the bottom right.
+
+![PXL_20240320_091559891](uploads/ce62ccda15052b530abb27f0d76a0e07/PXL_20240320_091559891.jpg){width=50%}
+
+6. Put on your sample and focus on it using the 'Locate' tab in the Zen Software (press 'Fluorescence' or 'Transmitted'). For this, the laser safety switch under the ocular has to be turned to 'visible' (open eye symbol)!
+7. With the front window open and the light in the incubator on (switch to the left, on the microscope table) you can safely navigate larger distances when using the joystick (which has an inverse logic). 
 For the front flap you will need to open (to move flap up) and tighten (to keep the flap in place) the little red screw. Please handle this window with care! 
  
-All doors on the incubator need to be properly closed before you can start imaging in the Acquisition tab and the laser safety switch under the ocular has to be turned to 'visible' (open eye symbol) as otherwise the interlock is not released and the lasers will not be active. You can check for this: if one of the LEDs on the main controller is blinking, one of the laser interlocks has not been recognized. Unfortunately, there is no feedback which interlock is affected, so you need to check them all and potentially, open and close all doors again or even lift the condenser and put it back down.
+8. All doors on the incubator need to be properly closed before you can start imaging in the Acquisition tab and the laser safety switch under the ocular has to be turned to 'non-visible' (crossed out eye symbol) as otherwise the interlock is not released and the lasers will not be active. You can check for this: if one of the LEDs on the main controller is blinking, one of the laser interlocks has not been recognized. Unfortunately, there is no feedback which interlock is affected, so you need to check them all and potentially, open and close all doors again or even lift the condenser and put it back down.
 
 ![PXL_20240320_091545142](uploads/771b95ca313e0a923254dbf26539bca8/PXL_20240320_091545142.jpg){width=49%} ![PXL_20240320_092901039](uploads/abfc3c39fba668f2f6dfff165d7c3a91/PXL_20240320_092901039.jpg){width=49%}
 
-The system will be by default at 27°C to minimize drift. Use the oil for 30°C. Immersion oil bottles for 30°C and 37°C are stored in the incubator at the bottom right.
-
-![PXL_20240320_091559891](uploads/ce62ccda15052b530abb27f0d76a0e07/PXL_20240320_091559891.jpg){width=50%}
 
 ## Environmental Control
 [Zeiss_Elyra_Environmental_controls_01.pdf](uploads/9e4a1088f421fd1742a2dd0076f3a89a/Zeiss_Elyra_Environmental_controls_01.pdf)