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Axio Scan Z1
Axio Scan Z1 Operating Manual 1. Make sure the slide scanner switch on the back and on the front 2. Login to the computer with your NETID and IGB password 3. Start ZEN blue then clicks on ZEN slidescan 4. Load your slides into the trays, place your slides ...
Köhler Illumination
Köhler Illumination for Brightfield Köhler illumination is a method for evenly illuminating the sample with white light. This method is very important for brightfield imaging in widefield microscopy, and for using the T-PMT for confocal imaging. Brightfield ...
Axio Zoom V16 Operating Manual
Power ON Routine 1. Turn on X-Cite epi-fluorescence light source for fluorescence imaging 2. Turn on EMS3 box 3. On the SYCOP 3, the system will prompt you to calibrate the stage: click yes to perform stage calibration. Make sure there is nothing blockin...
Introduction
Minflux is a florescence imaging and tracking technique using a 2D doughnut or 3D bottle beam to localize switchable fluorophores to single digit nanometer resolution. Expanding on this Minflux turns on fluorophores using a 405 laser. This allows the microsc...
Superimpose images in Imspector
Goal: Superimpose confocal images Superimpose confocal image with Minflux image Note: Images can be combined if they have the same length and the same pixel size. In general, the pixel size of the Minflux image usually is much bigger than confocal image. As...
Separating two signal based on dcr (detector channel ratio) in paraview
Goal: to separate signal form 2 detectors (CY5 near vs CY5 far), especially when you have two dyes for example AF640 and AF680 1. Open image in Imspector 2. Minflux Data Panel → Data source: it is usually None, so you must select data source that you want ...
Tracking in ParaView
Goal: how to analysis tracking data in paraview 1 Imspector: open your image in Imspector 2 Minflux Data panel → select data set on Data source panel → Compile trace data (Trace data compiled on the bottom of Minflux Data panel) → then Launch Paraview ...
IGB Core Instrument LSM 900
405nm, 488nm, 561nm, 640nm excitation. Zen Blue file:///C:/Users/gfried/Downloads/EN_poster_Beampath-LSM-900_A1.pdf
FLIM module
LSM 900
FCS module
EMPANADA Guide
To begin, I would recommend that one starts with the official empanada guidebooks as located here: https://empanada.readthedocs.io/en/latest/empanada-napari.html Much of what I will be talking about is found here, but I will go over a few caveats that I've fo...
Reserve Instrument Time (Quick Access)
On the Main Dashboard you will see Quick Action Widgets Choose the +Reservation button on the the Upcoming reservations widget. Choose the instrument you want to reserve time on. You may need to add a filter and select/type the name of the instrument. ...
Reserve Instrument Time (Side Menu)
Click on the Reservations Tab on the menu to the left. Choose Schedule and click on the Filters button just above the calendar. Search or type in the name of the instrument you want to reserve. Change the calendar/timeline view with the menu on the ri...
Initiate Usage
If an instrument does not have a computer to log into, or has a Linux operating system, you will need to initiate tracking manually. There are two ways to do this - via computer or the bookitlab app. The instructions are essentially the same, but below are sc...
Purchase a Consumable
To add a consumable choose the "Consumables" menu item on the side bar on the left. Choose from the list of items. In this case, click "Embedding Station Block" A menu on the right will appear. Click "+ Log Consumables" Choose the quantity of the c...
Cancel a Reservation
To cancel a reservation, go to the calendar via the Reservations tab on the the left menu. Filter your selection by the instrument you want. Click on your reservation. On the reservation menu on the right, click "Cancel" at the bottom of the menu. A g...
Logging in to a computer with BookitLab
Log into Windows with your NetID and Active Directory password A pop-up to log in to BookitLab should appear. If it does not appear, try opening Zen or the software used to control the instrument you are logging into. When it appears it should populate you...
Accessing the Core-Server
In general the process for accessing the core-server is the same as before. General instructions can be found here: https://help.igb.illinois.edu/Core_Server_Access .Since we are logging in with BookitLab, the mapping of the drive to your Windows profile will...
Microscopy Effects on Images
Detectors: Array Detectors Cameras, CCD's EMCCD's Back thinned CCD's, CMOS, SCMOS These detectors measure photons and produce electrons in each pixel. The pixels are then readout as a serial list of values representing the photon intensity at each locat...