Imaging Resource
Standard Operating Procedure
Incucyte 1 room 123
The incucyte should only be accessed using gloves and appropriate lab coat. You should never
open the incycyte drawer when the scan active green light is on!!!!
If the incucyte is sitting idle then you can open the drawer.
You should be able to see from the laptop that is on the top of the incubator where the system is in
the scan cycle. The system if needed to be shut down for any reason it should also be shut down and
restarted using this laptop. Never just power off this system without shutting it down through the
laptop! This laptop is linked to the client server where your images are saved during the timelapse
run. At the end of your session it is recommended that you archive your data for safe keeping. This
client server is not backed up by our IT department!!!! You are responsible for your own data!
Time taken to run each scan. Current time in the cycle blue dotted line.
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Standard Operating Procedure
The incucyte supports a large range of different plate. For wound healing assays it is recommended
that you use Imagelock 96 well plates and essenbio scratch making tool.
Open the drawer and insert your plates. The incucyte can run with up to 6 plates. The more plates
and the more positions selected the longer the time interval will be. For example is you are running
a scratch assay with 2x 96 well plates it will take 38min to scan the plates. If you are running a large
number of scans the system will may also give you a warning message as it is not recommended to
do more than 700min of scanning in a day. With 2x 96 you are using 912 min. Anything under
1000min should still be ok although not recommended. You can fix this issue by adding a longer
time interval so the system has more time to cool down or by inserting a cool down slot in the cycle.
Place your plate into the incucyte making sure that A1 is on the top left side of the plate. Check the
plate is flat by pressing gently on top of the plate. Please note: You cannot scan empty wells. It is
also not recommended to scan a well that is less that 10% confluent as this can cause focus issues.
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Standard Operating Procedure
The incucyte software can be found on the M: drive in “incucyte FLR training folder” Click on the
Incucyte2011ARevGuiSetup” to install the software.
Double click on the incucyte icon on the desktop.
To connect to an incucyte select “Connect to an incucyte” and enter the IP address 172.21.233.71 is
the IP address of the FLR system that we have in the BAIR facility. If you want to view archives
data select” Browse to an Archive”
You will be asked to enter your user name and password. This is essenbio/essenbio
The software will now open up.
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Standard Operating Procedure
Select the “Schedule upcoming scan” tab. This will show you what scans are in progress on the
system and what position the plates are in for these scans.
Click on the position of the plate you have just loaded and under Vessel type select the correct
plate.
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Standard Operating Procedure
The plate will be shown with a predefined scan pattern. This pattern can be edited and saved for
future use using the “Edit scan pattern “tab. Once you have done this to ensure the incucyte receives
the updates scan schedule click Apply. If you forget to do this the information is not sent to the
incucyte!!!!!!!!
If you make a mistake and remove someone else’s plate by accident the plate can be reloaded
provided you have not applied the changes.
The person that has booked the incucyte on the beatson scheduler can use as many of the plate
positions as they require. If there is spare capacity you may asked the user that has booked the
system
Under the properties tab enter your
name_ group and date.
Cell type and any other notes
required.
A plate map can also be loaded at
this point. The plate map is made
using the incucyte plate map editor
software which is a separate
software programme. It can then be
saved for use with your plates.
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Standard Operating Procedure
Plate map editor. See MOP or TG for how to use this.
Remember to apply any updates or the incycyte server will not be sent the updates information
If you are starting a new run where no plates but your plates are on the incucyte and you have
booked the system on the scheduler you can change the time interval to suit your needs. Right hand
mouse click on the time line and
If 24hr is selected it will run until
stopped. Under add scans select
time interval required. Select ok .
Again remember to apply the
changes made or the incucyte server
will not update the run.
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Standard Operating Procedure
Under “Find Scanned Vessels” all completed scans of each plate can be found.
Under this tab you can select each plat for analysis. All analysis must be done while your data is on
the incucute server. Once you have analyses your data and archived it you can view the archived
data and the analysis offline without being connected to the server. You cannot however preform
any further analysis without re loading the archived data back onto the server. This archiving and
reloading of data can take some time but the server in not large enough to leave and store your
important raw data here. You must back up your raw data( original TL run with all the images)
onto our network where it will be backed up by IT. Once you have done this please delete your
data off the incucute server. If we find the server full or data that has been left on the
server for longer that one month we will delete it!
Double click on the data you with to analyse. This will open up another window displaying this data
and the images associated with each time point.
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Standard Operating Procedure
Click on the individual time points to see the individual images in the window. You can also play
them as a slide show movie. To archive this plate select utilities and “Archive Current Vessel”
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Select the network area where you want to archive the file to. I would select your own N: drive.
Select “Archive vessel” when it is complete you will see a message alerting you if there were any
errors. Archiving in this way will archive one well at a time.
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Standard Operating Procedure
You can also archive all 6 incucyte plates at the same time by selecting “ administer incucyte”
Select the Scan tab
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Standard Operating Procedure
Select a destination folder and the scan days to be archived and “archive scans”
Archived data can also be restored onto the incucyte server using “restore from archive” under the
task drop down menu.
After archiving your data please check that the data can open offline and is ok before you delete it
from the Incucyte HD.
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