The first step in creating your customized spectra-viewer ("microscope page") is to gather the information about your instrument that you will need. This includes:
Light source(s), such as an LED or metal-halide light engine, or laser wavelengths
Excitation, dichroic (beamsplitters) and emission filters. You will need the actual brand and model number (for Chroma and Semrock) filters, or you will need to have the spectrum information available.
If you don't know exactly what fluorescence filters you have in your instrument, then you've got to do some digging. Most mounted commercial filters will have the necessary information printed on the side of the filter, though dichroic filters are often unlabeled.
In a conventional microscope, your filters will often be in a filter cube inside the filter turret. Alternatively, your excitation filters and/or emission filters may be mounted in external filter wheels.
Chroma part numbers will often be named something like ET525/50x, whereas Semrock part numbers typically look something like FF03-525/50. Though in each case, there are many variations.
Next, you need to assemble a list of the different optical configurations that you use to image different fluorophores on your microscope. By "optical configuration" here, we are referring to a combination of light source, filters, and camera (these usually correspond to buttons or settings in your microscope software that put the appropriate hardware into the optical path). Here's an example of how such a table might look:
It's possible that a single filter (particularly multi-band dichroic filters) will be used in more than one optical configuration on your microscope.
You can create a new microscope at FPbase at https://www.fpbase.org/microscope/create/
After providing a name and (optional) description for your microscope, there are two ways to enter optical configuration information:
In Bulk: This lets you enter everything as text, which can be much faster, particularly for a first-time setup, but it is more error prone, and requires that all the filters are already in the database. It's worth a try, then fall back to the manual form entry if necessary.
One config at a time: Here, you select filters in each optical configuration in corresponding selection fields in the form. Slower, but less error prone.
I recommend starting here, and resorting to the manual entry if you run into errors that cannot be easily fixed. To, add configs in bulk, select the middle tab
Bulk configs must be entered in the correct format: one config per line on a separate line, using the following 4 or 5 field comma-separated format:
Name, Laser OR Ex Filter(s), Dichroic(s), Em Filter(s) [, Dichcroic reflects ex?]
Commas are considered delimiters, and are not allowed in names. Lasers must be entered as integer values. Any broadband light sources entered in the "Light Source(s)" field, or cameras entered in the "Detector(s)" field will be applied to all of the configs, but leave them out of the text entry. (If you don't want the light source on all configs, you will have to add it manually later). For example, the two configs shown in the table above would be entered as follows:
Green, ET470/40x, T495lpxr, ET525/50mRed, FF01-543/22, FF562-Di03, FF01-593/40
Most microscopes have a dichroic that is oriented such that it reflects excitation light to the sample, and passes emission light to the detector. Others (most commonly seen on a Yokogawa spinning disc confocal), have the dichroic in the opposite "inverted" arrangement, such that it reflects the emission light. An optional 5th item ("true" or "false") specifies whether the dichroic reflects excitation light. For example, a Yokogawa setup might look like this:
Yokogawa 488nm, 488, Di01-T405/488/568/647, ET525/50m, false
In some cases, you might have multiple sequential filters in the same "role" (excitation or emission). For instance, some light sources have excitation filters inside of the light source, and you may also have a filter elsewhere in your light path. Alternatively, image splitting devices sometimes have a dichroic in the emission path as well as a cleanup-barrier filter. Multiple filters in a given part of the light path can be indicated by enclosing them in parentheses. For example, a TIRF scope that has a notch filter in addition to a barrier filter in the emission path:
TIRF 647nm, 647, ZT405/488/561/647rpc, (ZET405/488/561/647m, ET700/75m)
This is the default method (first tab), and allows finer-tuned control over each optical config, and is a bit less error-prone than the bulk method. It is pretty self-explanatory: just enter the appropriate filter, or laser/light source/camera in the appropriate field in the optical config. Multiple filters can be entered in each of the fields. If a filter does not exist, you can try to import it with the "import commercial filter" button, otherwise you will have to upload it manually. To add additional configs, click the "Add Optical Config" button.
As described above, some dichroic filters are arranged such that they reflect (rather than transmit) emission light. If that is the case (such as on most Yokogawa systems), click the "reflects em" box above the dichroic filters.
Often in simultaneous dual-channel (image-splitting) setups, there is a (usually longpass) dichroic filter in the emission path that reflects shorter wavelengths. In that case, you may add the dichroic filter to the "Advanced: Reflective Emission Filter(s)" field (e.g. for the shorter wavelength in a simultaneous dual-channel setup).
The third tab allows you to enter additional components that you would like to have available, but which you don't want to have associated with any particular optical config