Histology Lab moved from Marsh Lab #12 to Health Sciences Building #263A.

The Cellular Analysis Facility (CAF) in the Department of Microbiology and Cell Biology, located in the Health Sciences Building, is focused on the analysis of the phenotype and function of cells and tissues by flow cytometry, histology, and single cell transcriptomics (scRNA Seq). We provide instrumentation including FACS analyzers, a FACS sorter, an imaging cytometer, a tissue processor and embedder, microtomes and cryostats, fluorescent microscopes, and a 10x Genomics Chromium Controller, as well as user training and core services. Facility Director Diane Bimczok, DVM, PhD, can be reached at 406-994-4928 or [email protected]

The Core Facility is located in the Health Sciences Building, HSB 247 and HSB 241.

One of the flow cytometers is located in the Cooley building (room 29) to for easy access by researchers on campus.

The histology core facility is currently located in the Health Sciences Building #263A.

We plan to move the instruments used for histological services to HSB 263A to facilitate instrument access and maintenance.

For more information contact Andy Sebrell at 406-994-2878 or [email protected].

Core Facility Instrumentation

ZE5™ Cell AnalyzerS

The new ZE5 is equipped with five lasers and filters to analyze up to 27 colors, plus forward and side scatter. The ZE5™ has a fully integrated, automated sample loader, compatible with all standard tubes and culture plates; has a specialized small particle (20 nm to 1 µm) analyzer for microbiology, virology and exosome research.

ZE5 information

Features of the ZE5 Cell Analyzer: Sample loading system:

  • Universal sample loader: easily switch between tubes, 96-well plates and 384-well plates with no hardware changes using the integrated sample loader.
  • Temperature control and orbital agitation
  • Sample pump with minimal dead volume and sample recovery feature
  • Automated plate reader can read a 96-well plate in 15 minutes and a 384-well plate in 60 minutes
  • Can analyze up to 100,000 cells per second

Stratedigm SE520EON

The SE520EON is a 2-laser (488 nm with 530, 580, 676 and 780 nm detectors and 640 nm with 676 and 780 nm detectors), 6-color fixed configuration system.

BD FACS Caliburs

Two FACS Calibur analyzers are available for basic cell analysis, with one instrument located in the HSB FACS Core room and a second one in the Cooley building (Cooley 29). The FACS Caliburs are equipped with two lasers (488 nm and 642 nm), allowing the analysis of up to 6 different cell parameters

BD FACS Aria II cell sorter

The FACS Aria is a high-end 8- to10-parameter flow cytometer with high-speed cell sorting capability.  The FACS Aria is contained within a biosafety cabinet allowing for sorting of BSL-2 level-infected or primary human samples.

FACS Aria 2 Cell Sorter

Detailed laser/detector configurations for each cytometer may be found at https://fluorofinder.com/.  Select "Montana State University."

Sign up for a slot by visiting the Google Calendar here or emailing [email protected]

ImageStream imaging cytometer

Imaging cytometry (ImageStream) combines features of flow cytometry and high-resolution light and fluorescent microscopy analysis of cell suspensions to capture images for each event passing through the detector in a flow stream.  The ImageStream ISX Mach II imaging cytometeris equipped with three lasers (488/642/785 nm) to record six image channels per object (bright field, dark field and 5 fluorescence channels), a multiple magnification option (20x, 40x and 60x) to image both eukaryotic cells and bacteria.

ImageStream Mark II

10X Genomics Single cell RNA sequencing

Single Cell Sequencing (scRNASeq) is as a novel, state-of-the-art approach that enables comprehensive analyses of heterogeneous cell populations and that is revolutionizing transcriptomics studies.

The 10x Genomics Chromium Controller is a user-friendly droplet-based scRNA-seq system that enables processing of up to 80,000 individual cells in up to 8 samples for downstream RNA sequencing in one single experiment. The Chromium Controller uses drop-based microfluidics to label individual cells in a suspension with genetic barcodes. This barcoding process enables researchers to identify all cDNA sequences from a single cell upon sequencing, based on their unique molecular identifiers.  The Chromium platform also is compatible with other single-cell, sequence-based analysis approaches such as studies of chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, and CRISPR edits.

10x Genomics Chromium Controller

10X Genomics provides a free, easy-to-use analysis and visualization software specifically designed for the complex datasets generated with the Chromium scRNASeq workflow that enables researchers to access, explore and interpret their data.

10x Genomics Workflow

Flow Cytometry*

FACS Aria II Sorter – sorting service



FACS Aria II Sorter – user operated






ZE5 Cell Analyzer



Stratedigm SE520EON



BD CytoFlex# (Under Repair)



BD FACS Calibur






Embedding station









Staining station (deparaffinizing and H & E) 



Chromium Controller



Histology Facility

The histology core facility provides histological services using standard histological techniques. The histology core is part of Microbiology and Cell Biology and is located in the Health Sciences Building #263A. The core can provide paraffin and frozen sections, Immuohistochemistry, processing, embedding, and routine staining of tissues by the staff (fees provided below). With approved training, individual lab personnel may also use the equipment for a fee. 

Leica cryostat photo #1

The histology lab has a Leica cryostat for sectioning frozen sections and a VIP6 processor which dehydrates tissues for paraffin sections.

Histopathology Fees

Paraffin Processing: 

Tissues submitted to the lab in 70% ETOH (no Formalin, NBF) in labeled cassette or container if you don’t have cassettes. Histology lab will make sure the appropriate size cassette is used before processing. If processing very small samples such as mouse eyes, Organoids, or similar sized tissues please make sure to use cassettes with smaller vents. Tissues will shrink and can be pulled through the vents if too large while processing.

Tissue submitted in 70% ETOH, processed and embedded                                     $6.00 per cassette

Processing                                                                                                                         $4.00 per cassette  

Embedding                                                                                                                        $2.00 per cassette

Unstained Section on one slide                                                                                     $1.50 per slide

H & E stained slide                                                                                                           $2.50 per slide

TRAP stained slide (PI supplies the reagents)                                                              $4.00 per slide

Toluidine Blue Stained slide                                                                                           $2.50 per slide

Giemsa, Masons Trichrome                                                                                            $10.00 per slide

PAS TUNEL Stain (PI supplies reagents)                                                                        $6.00 per slide                                                                                                                                      

Special requests for stains if dyes must be ordered -cost dependent                    Price TBD

Immunohistochemistry stains requiring enzyme digestion or                                 $12.50 per slide

Antigen Retrieval of paraffin embedded tissue.  (PI supplies Antibodies)                       


Usage of Facility equipment and stations:

Processing                                                                                                                          $4.00 per cassette

Embedding station                                                                                                           $1.00 per cassette

Microtome                                                                                                                        $15.00 per hour

Cryostat                                                                                                                              $20.00 per hour

Staining station (deparaffinizing and H & E)                                                               $10.00 per hour


Frozen Sectioning:

Snap freezing tissues                                                                                                      $5.00 per block

Unstained frozen section                                                                                                $1.50 per slide

H&E stained frozen section                                                                                             $2.50 per slide


Bone Histotechniques:

Decalcification 15% Formic Acid                                                                                   $1.50 per tissue/cassette

Decalcification EDTA                                                                                                      $2.50 per tissue/cassette

Leica microtome photo #2

The lab has a Leica microtome for sectioning paraffin embedded tissue. There is also a Tissue Tek paraffin embedding station.

Histology lab photo #3

Histology lab has a slide staining station set up for immediate use. 

For more information contact Andy Sebrell at 406-994-2878 or [email protected] or Diane Bimczok at 406-994-4928, [email protected].