Tissue Processing and Embedding Services for FFPE and Frozen Samples

iHisto provides comprehensive tissue processing and embedding services for both formalin-fixed paraffin-embedded (FFPE) and frozen samples. Our experienced team handles fixation, dehydration, clearing, paraffin or OCT embedding with precision—ensuring consistent quality for downstream applications like H&E, IHC, IF, and ISH.

🧬 Overview 

Tissue processing and embedding is the first and most critical step in histology. Proper fixation, dehydration, clearing, and paraffin embedding preserves cellular detail and morphology — laying the foundation for all staining and imaging workflows.

At iHisto, we support both routine FFPE workflows and custom protocols for various tissue types:

• Human, rodent, primate, xenograft, and biopsy tissues

• Standard and large-format blocks

• Fatty, calcified, or delicate specimens

• Client-supplied cassettes or loose tissue samples

All processing is performed using automated closed-system processors for optimal consistency and tissue preservation.

⚙️ Our Tissue Processing Workflow

1. Sample Receipt & Logging
   Barcode tracking and visual inspection for sample integrity

2. Fixation
   Standard 10% NBF or custom fixatives upon request

3. Automated Dehydration & Clearing
   Using alcohol and xylene or xylene substitutes

4. Paraffin Infiltration
   Vacuum-assisted infiltration using validated reagent cycles

5. Tissue Embedding
   Accurate orientation into paraffin blocks using heated embedding centers

6. Block Labeling & Storage
   Blocks labeled and optionally stored or prepared for sectioning

🧪 Applications of Our Embedding Services 

iHisto provides both formalin-fixed paraffin embedding (FFPE) and OCT-based cryo embedding, supporting a wide range of histological and molecular applications:

• Routine H&E staining – for FFPE or frozen section morphology

• Immunohistochemistry (IHC) and in situ hybridization (ISH) – compatible with paraffin or cryosection workflows

• Special stains and board-certified pathologist review

• Biobanking and long-term archival – FFPE blocks or cryobanked OCT tissue for future reanalysis

• Molecular pathology workflows – RNA/DNA-safe processing for PCR, sequencing, or ISH

• Spatial biology & multiplex assays – embedding optimized for platforms like 10x Visium, NanoString GeoMx, and RNAscope®, across FFPE and fresh-frozen formats

📏 Fixation Cheat-Sheet

Below are quick, specimen-specific guidelines for fixative choice and immersion time. All recommendations assume room temperature and a fixative volume that is at least 15–20 × the tissue volume.

Brain (cortex, cerebellum)

Fix in 10 % neutral-buffered formalin (NBF) or 4 % paraformaldehyde for 24–48 h. Slice to ≤ 5 mm; going beyond 72 h can mask certain phospho-epitopes in IHC.

Eye / whole globe

Begin in Davidson’s solution, then transfer to NBF or 70 % ethanol. Total time 12–48 h (≤ 24 h for small animal eyes) to prevent retinal detachment and lens distortion.

Testis / epididymis

Bouin’s solution (or modified Davidson) for 6–24 h yields crisp nuclear detail; rinse picric acid thoroughly before processing.

Breast core or surgical resection

Standard 10 % NBF, 6–72 h, meeting CAP/ASCO requirements for ER/PR/HER2 scoring.

Lung

Perfuse or immerse in NBF for 12–24 h; instill fixative to keep alveoli inflated.

Liver

10 % NBF, 12–24 h. Trim to ≤ 3 mm thickness; transfer to 70 % ethanol if downstream molecular assays are planned.

Kidney

10 % NBF for 4–24 h. Bouin’s enhances PAS staining but is less DNA-friendly.

Spleen / lymph node

10 % NBF, 6–24 h. Because of high blood content, maintain a ≥ 20 × fixative-to-tissue ratio to avoid edge artifacts.

Heart

10 % NBF, 24–48 h. Section transversely through ventricles; perfusion is preferable for embryonic hearts.

Skeletal muscle biopsy

Either snap-freeze immediately for enzyme histochemistry or fix thin strips in NBF for 2–4 h. Longer formalin times can swell fibers.

Skin / soft tissue

10 % NBF, 6–24 h. Limit to < 24 h if SOX10 or Melan-A IHC is anticipated.

GI tract (stomach, colon)

10 % NBF, 6–24 h. “Bread-loaf” thick resections to ≤ 5 mm to prevent mucosal autolysis.

Bone marrow trephine

Acetic acid–zinc formalin followed by rapid EDTA decalcification: 24–48 h fixation plus 2–4 h decalcification balances morphology and antigenicity.

Cortical bone (e.g., femoral head)

Fix in NBF for ≥ 72 h, then decalcify in EDTA or formic acid for 7–14 days. Refresh decalcifier regularly for uniform softening.

Accelerated methods (microwave, ultrasound, pressure) can shorten these times, but each lab must validate the impact on downstream assays.

Quick Tips for Reliable Fixation

1. Slice or perfuse whenever possible—formalin penetration is roughly 1 mm per hour.

2. Document “in” and “out” times for GLP or CAP traceability.

3. Move blocks to 70 % ethanol after 24 h when long-term storage is expected to halt additional cross-linking while keeping tissue firm.

✅ Why Choose iHisto

• ✅ Clean, artifact-free blocks with precise orientation

• ✅ Fully automated processing using top-tier systems (e.g., Leica, Sakura)

• ✅ Compatible with downstream IHC, ISH, and spatial biology

• ✅ Low-volume and high-throughput capacity

• ✅ Optional slide sectioning, staining, and digital scanning services

• ✅ Experienced in both GLP and research-only workflows

❓ FAQs 

• What is tissue processing in histology?

Tissue processing involves fixing, dehydrating, clearing, and infiltrating tissue samples before embedding. This prepares tissues for microtomy and staining. iHisto offers reliable processing for both FFPE and frozen workflows.

• What embedding options are available at iHisto?

We offer paraffin embedding for FFPE samples and OCT embedding for frozen tissues. These methods ensure sample stability for sectioning and downstream analysis such as H&E, IHC, and IF.

• What types of tissue does iHisto accept for processing?

iHisto accepts a wide range of animal and human research tissues. Samples should be submitted either fresh (for fixation) or pre-fixed in formalin. Frozen tissues must be shipped on dry ice.

• What is the turnaround time for processing and embedding?

Our standard turnaround time is 3–5 business days. Faster turnaround may be available depending on sample type and workload.

• How do I submit tissue samples to iHisto?

Contact us at info@ihisto.io or submit a request via our website. We will provide detailed submission instructions, including recommended fixatives, labeling, and shipping protocols.

📩 Request a Quote or Consultation 

Need reliable, high-quality tissue processing and embedding? iHisto is your trusted partner for FFPE sample preparation — from fresh tissue to paraffin block.

👉 Request a Quote or email us at info@ihisto.io