We are trying to image cells using multiple fluorescent channels. Currently we can change the filters on the microscope by hand but when we tell the program to take a photo of multiple channels it does not change the filter, so on the acquired image the same picture is being imaged for all our selected channels. Are we missing pressing a button or is there a configuration error? In the future we would like to be able to image 3 fluorescent channels and brightfield at the same time, is this possible?
Thank you, Alicia
Automated 3 fluorescent and 1 brightfield channel is certainly possible in Micro-Manager. That is more or less what it was designed to do.
The Micro-Manager website (https://micro-manager.org) is full with information on how to configure and use the software. Highly abbreviated: you will need to define “Configuration presets” for your fluorescent and brightfield channels. You should be able to select a specific channel by clicking on the setting, and choosing the new setting from the drop-down box. When you configure this (start with the “Group +” button), include the “Core-Shutter” property to switch between brightfield and fluorescent shutter.
Once you have that set-up correctly, click on “Multi-D Acq”, select the “channel group” that has your presets, and you are ready to go.
I you still have questions after reading the documentation Nico posted, why don’t you send you config file and we can see if someone can offer pointers there.
Thank you for the replies. I’m still having some problems getting this to work. I can add a new group and have put on the core shutter but I am still having problems with the program switching the shutters. I have added our configuration below.
Generated by Configurator on Fri Sep 30 16:48:48 PDT 2011
Pre-init settings for devices
Pre-init settings for COM ports
Hub (parent) references
Label,Objective,3,Nikon 20X Plan Fluor ELWD
Label,Objective,1,Nikon 10X S Fluor
Label,Objective,0,Nikon 40X Plan Flueor ELWD
ConfigGroup,System,Startup,Objective,Label,Nikon 10X S Fluor
Resolution preset: Res20x
ConfigPixelSize,Res20x,Objective,Label,Nikon 20X Plan Fluor ELWD
Resolution preset: Res40x
ConfigPixelSize,Res40x,Objective,Label,Nikon 40X Plan Flueor ELWD
Resolution preset: Res10x
ConfigPixelSize,Res10x,Objective,Label,Nikon 10X S Fluor
The configuration you posted is the “demo” configuration with an added Hamamatsu camera. The “demo”/“virtual” equipment will not do anything (other than simulate hardware), so do not expect anything to happen. Start with a new configuration file with the Hamamatsu camera and your other equipment. Once you define your “channel” group, add the “Core”-“Shutter” property. That property lets you switch the “active” shutter.