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====Checking cells under microscope==== *Make sure everything is on for the microscope (modules 1,2,3,4) *Open up Micromanager 1.4 program (press okay when MCS popup window shows up) *Open up C1 plugin ("C1 autocapture and processing" window) and perform the following steps: 1) Position initialization Chamber = 1 -> "set" (look at "live" in original micromanager program) (This will set the initial position 1) 2) Focus recorder (setting focus to all 4 corners = can only set focus if there is a cell in the capture site so move to the next closest well that contains cell) L Top -> 1 "Goto" "Get" (when in focus) L Bottom -> 46 "Goto" "Get" R Top -> 87 "Goto" "Get" R Bottom -> 96 "Goto" "Get" 3) Channels (keep as default) Brightfield Exposure = 8 Dapi Exposure = 20 Slice # = 3 Capture Range: Begin = 1 Z step = 10um End = 96 Output Folder = (You need to specify) = will output raw images into a "Source" subfolder then "Processed" subfolder will contain overlays 4) Before hitting acquire, move to 1st position (using "goto" for L Top) 5) "Acquire" = will take first the brightfield images then the DAPI
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