Fluorescence

Before asking for fluorescent slide scanning you should get acquainted with both the fluorochromes you use and the filters we have: because the match between filters and fluorochromes is not a given match.
Below is a table of the filter combination we have (click on the filter link to see tech specs) and for each of them the best fluorochromes you can chose.
Before you select the fluorochromes to be acquired or to check the compatibility of the ones you already have, register and practice with the tool provided by the filter company Semrock: SearchLight.
Registration is free.
Here you can view/download an example of the analysis of several orange fluorochromes with the filters we have on the Aperio FL.
You may also take a look at the list of fluorochromes on the page of the Center for Cytometry and Molecular Imaging of the Salk Institute.
We can help you choose the best fluorochrome-filter combo.
Fluorescent whole-slide images (FL-WSI) are forever to keep: ask for our prices to scan a fluorescent slide for you.
We are able to stain routinely fixed and embedded section with three antigens and a nuclear counterstain in four distinct immunofluorescent non-overlapping colours. Here you may download an example of 4 color lymphoid tissue staining and here an example of 4 color staining of a benign skin lesion for p16, Ki-67 and S-100.

Filter Peak  ą Range Sensitivity Fluorochromes
Excitation nm (molecules/cell)
Semrock  377 53 324 - 430 approx.50K Alexa FluorŪ 405, BV421
Aperio FL 387 11 376 - 398 NA DAPI
Aperio FL 485 20 465 - 505 10K Alexa FluorŪ 488, FITC, SYTOX Green
Aperio FL 560 25 535 - 585 2K RhodamineRedX, Alexa FluorŪ 568, DyLight 549
Cy3.5-A-Basic 565 24 541 - 589 2K RhodamineRedX, Alexa FluorŪ 568, DyLight 549
Aperio FL 650 13 637 - 663 2K Alexa FluorŪ 647, 660, 680, Cy5.5
Emission
Aperio FL Quadband 440 40 400 - 480 approx.50K DAPI' Alexa FluorŪ 405, BV421
Aperio FL Quadband 521 21 500 - 542 10K Alexa FluorŪ 488, FITC, SYTOX Green
Aperio FL Quadband 607 34 573 - 641 2K RhodamineRedX, Alexa FluorŪ 568, DyLight 549
Cy3.5-A-Basic 620 52 568 - 672 2K RhodamineRedX, Alexa FluorŪ 568, DyLight 549
Aperio FL Quadband 700 45 655 - 745 2K Alexa FluorŪ 647, 660, 680, Cy5.5

Aperio FL Quadband is a quadriband emission filter. For some fluorochrome combo you may need separate emission filters (e.g. Orange and Red).
Sensitivity of the instrument is a measurement which do not takes into account antigen availability in case of direct/indirect immunofluorescence.
Note that tissue autofluorescence will decrease your sensitivity by increasing the background; Green>Orange>Blue>Red are the tissue autofluorescent channels in decreasing order of magnitude.

Tutorials

The best website containing detailed and clear tutorials on all aspects of microscopy and fluorescence is Microscopy-U (Nikon).
Molecular Probes: The Handbook (Invitrogen) is also an excellent reference website.
Fluorescence fundamentals is notable form beginning to the end.
Purdue University Cytometry Labs has a series of on-line teaching lessons in PowerPoint.
Olympus hosts a Molecular Expressions website.