TissueFAXS SL Fluorescent Slide Scanner

Specifications

  • TissueGnostics scanner with 120 slide loader and Zeiss upright microscope
  • Fast scanning of whole slides
  • Air objectives: 2.5x/0.09, 5x/0.16, 10x/0.45, 20x/0.5, 20x/0.8, 40x*/0.95
  • Oil objectives available upon request: 40x/1.3, 60x/1.4
  • Up to 7 fluorescent tags, including near IR (Cy7)
  • Sensitive back-thinned sCMOS monochrome camera (Hamamatsu ORCA-Fusion BT C15440)
  • Paired with StrataQuest workstation (Marlin) for whole-slide analysis

*Please use #1.5 coverslips with the the 40x/0.95 air lens

Sample Preparation

  • Scan area is limited to 50mm from clear edge

  • Do NOT use antifade/mounting media with built-in DAPI*. Buy mountant without DAPI and do a separate DAPI stain and wash!!

  • Do NOT freeze your stained slides. Re-freezing slides will destroy your samples. Once stained, store them at 4°C.

  • Do NOT use the following flow-cytometry dyes. Some flow dyes and reagents do not work for imaging – especially with multi-band filters. Choose alternatives to these broad-spectrum dyes

    • ❌❌ PE (Phycoerythrin)
    • ❌❌ PerCP
    • ❌ APC (Allophycocyanin) - Cy5 or AF647 are preferred
    • ❌❌ Quantum Dots
    • ❌❌ Brilliant UV/Violet dyes other than BV421

  • Camera/filter scanning settings apply per-slide. Use one set of fluorescent dyes per slide.

  • See filter list below for recommended fluorescent dyes

  • Use a #1.5 coverslip over your sample

  • Use an antifade mounting media (but one without built-in DAPI*)

  • Blank magazine layout template available in WORD and PDF formats

*Antifade with built-in DAPI is meant for high-volume clinics. Never buy it for research. The DAPI goes bad very quickly, diffuses into tissues poorly, and always leaves a background signal. Instead, do a separate DAPI stain and wash out the excess before mounting. Why spend hours, days, or months on an experiment and ruin it at the last minute with a poor reagent when a 5-15 minute DAPI stain will work much, much better!

Two Scanning Software Configurations

AllBand (slow scanning) and QuadBand (fast scanning)

AllBand Fluorescent Filter Configuration

Slower scanning using partially separated filters, filters can be mixed-and-matched

Chroma single band DAPI, low bleed-through, better nuclear separation

Name #* Std dyes
DAPI 5 DAPI/Hoechst

*NOTE: # indicates filter cube position. Multi-band filters have the same position #s

Chroma wide-band, bright, up to 5 colors

Name # Std dyes Cy series Alexa
mDAPI 6 DAPI/Hoechst/BV421
mFITC 6 FITC Cy2 AF488
mTRITC** 6 TRITC Cy3 AF546
mTxRed** 7 RFP/TxRed Cy3.5 AF594
mCy5 6 APC Cy5/Cy5.5 AF647
mCy7 7 Cy7 Cy7 AF750

**NOTE: mTRITC and mTxRed filter have overlapping spectra. They are mutually exclusive

Spectra-Split narrow-band, better separation, up to 7 colors

Name # Std dyes Cy series Alexa Opal Atto Dylight
ss380 1 DAPI/Hoechst/BV421      
ss440 4 BV480     Opal p 480 Atto425  
ss488 1 FITC Cy2 AF488 Opal 520 Atto488 Dylight488
ss546 2 TRITC Cy3 AF546 Opal 570 Atto542 Dylight549
ss594 3 TxRed   AF594 Opal 620 Atto590 Dylight594
ss647 4 APC Cy5/Cy5.5 AF647 Opal 690 Atto647 Dylight647
ss750 1 Cy7 Cy7 AF750 Opal p.780 Atto740 Dylight750

QuadBand Fluorescent Filter Configuration

Very fast scanning with Chroma multi-band filter, up to 4 colors without filter change delays

Name # Std dyes Cy series Alexa
mDAPI 6 DAPI/Hoechst/BV421  
mFITC 6 FITC Cy2 AF488
mTRITC 6 TRITC/TxRed Cy3 AF546/594
mCy5 6 APC Cy5/Cy5.5 AF647

Extended Depth of Focus

Recommended Z-step sizes for extended depth-of-focus imaging

Objective Z Step
10x/0.45 4.0 µm
20x/0.5 2.5 µm
20x/0.8 1.0 µm
40x/0.95 0.8 µm
40x/1.3 Oil* 0.6 µm
63x/1.4 Oil* 0.5 µm

*Limited availability. See staff for oil objective use