- [Resource Hub](/) - Field Guides # Field Guides 38 resources ## All Resources Filters Clear All Resource Type Field Guide Instrument Moxi GO II Moxi V Moxi Z Singulator 200+ Application Assay Standardization Bioprocess Development Cell Manufacturing Cell Viability Endpoint Counting Functional Assay Immunology Oncology PBMC Analysis FFPE Tissue Neuroscience Single Cell Genomics Tissue Dissociation Drug Discovery Tissue Type Brain/CNS Downstream Application 10x Chromium Flex Cell or Nuclei Nuclei Showing 38 of 38 resources Filters [Field Guide](/resources/01-invisible-contaminants/) ### Invisible Contaminants Every cell preparation contains some level of debris—fragments from lysed cells, extracellular matrix remnants, aggregates, and other particulate matter—that quietly skews counts and downstream results. [Read Field Guide](/resources/01-invisible-contaminants/) [Field Guide](/resources/01-optimization-burden/) Moxi GO II Moxi V ### The Optimization Burden: Hours Wasted on Viability Protocol Development Every hour spent optimizing viability dye concentrations is an hour not spent on your actual experiments. It's optimized for use - that's the important thing. You don't have to optimize it as a customer. Pre-optimized viability reagents eliminate the titration experiments, the incubation testing, the cell-type-specific protocol development. Why spend time optimizing when validated performance is available from the first use? [Read Field Guide](/resources/01-optimization-burden/) [Field Guide](/resources/02-unknown-product/) Moxi GO II Moxi V ### The Unknown Product: Most Moxi Users Don't Know This Exists Most of the issue with viability reagents is that most people don't even know they exist. If you're running viability assays on Moxi V or Moxi GO II with generic dyes you optimized yourself, there's a better option you may not have heard about: pre-optimized, ready-to-use viability reagents designed specifically for your instrument. Now you know. [Read Field Guide](/resources/02-unknown-product/) [Field Guide](/resources/03-ambient-rna-soup/) ### Ambient RNA Soup Single-cell genomics platforms capture transcripts from individual cells to reveal heterogeneity that bulk methods miss. That resolution depends on clean single-cell suspensions, where ambient RNA from lysed cells can contaminate every droplet. [Read Field Guide](/resources/03-ambient-rna-soup/) [Field Guide](/resources/03-dilution-math/) ### The Dilution Math Problem: Every Calculation Is a Potential Error Consider a simple 1:100 dilution from stock. Errors can enter at multiple points—stock measurement, diluent measurement, mixing adequacy, transfer losses—and each step compounds into measurable variability. [Read Field Guide](/resources/03-dilution-math/) [Field Guide](/resources/04-compounding-viability-errors/) ### Compounding Viability Errors Most researchers assume that adding viability stains improves the accuracy of their cell counts. After all, you're adding more information—shouldn't that make the measurement better? The reality is more complicated. [Read Field Guide](/resources/04-compounding-viability-errors/) [Field Guide](/resources/04-protocol-hunt/) Moxi GO II Moxi V ### The Protocol Hunt: Searching for Methods That Already Exist Searching for viability protocols, adapting literature methods, trial-and-error until something works - this is time you don't need to spend. The user manual is designed to be super easy. Concentration-based instructions tell you exactly what to do: put X amount of viability reagent and put X amount of sample, incubate and go. No protocol hunting required. [Read Field Guide](/resources/04-protocol-hunt/) [Field Guide](/resources/05-dissociation-damage-blindspot/) ### The Dissociation Damage Blindspot: Viability Assessment Reveals Protocol Impact A protocol can achieve high cell yield while producing low cell viability. Aggressive dissociation that frees many cells may simultaneously damage or kill them—a blindspot that viability assessment exposes. [Read Field Guide](/resources/05-dissociation-damage-blindspot/) [Field Guide](/resources/05-diy-mentality/) Moxi GO II Moxi V ### The DIY Mentality: When Making Your Own Viability Reagent No Longer Makes Sense That's why people - including me - just buy premixed gel loading dye and don't make my own from powder like my PI wanted me to. The same logic applies to viability reagents. Buy the damn gels rather than making them - consistency and data. When convenience and consistency matter more than tradition, pre-made beats DIY. [Read Field Guide](/resources/05-diy-mentality/) [Field Guide](/resources/05-missing-qc-checkpoint/) ### Missing QC Checkpoints Every laboratory has protocols for cell culture, staining, and instrument operation. But ask about sample quality standards—specifically, debris thresholds—and you'll often find a blind spot where a QC checkpoint should be. [Read Field Guide](/resources/05-missing-qc-checkpoint/) [Field Guide](/resources/05-suboptimal-resolution/) Moxi GO II Moxi V Moxi Z ### The Suboptimal Resolution Problem: Why Your Cell Populations Look Merged Using an aperture much larger than necessary reduces sizing resolution by creating smaller signal differences between cell sizes. Cell populations that should be distinguishable appear merged when the aperture is too large for the cells being measured. Target 15-40% of aperture diameter for optimal resolution. If you're counting lymphocytes on M+ cassettes because it works, you're sacrificing the sizing resolution that S+ cassettes would provide. [Read Field Guide](/resources/05-suboptimal-resolution/) [Field Guide](/resources/06-batch-consistency/) Moxi GO II Moxi V ### Viability Reagent Batch-to-Batch Consistency: Why Your Results Vary Over Time When you make your own viability reagents, every batch is different. When you buy pre-optimized reagents with QC'd lot consistency, every lot performs the same. Long-term experiments need long-term consistency - and that consistency comes from manufacturing quality control, not from hoping your technique stays identical over months of work. [Read Field Guide](/resources/06-batch-consistency/) [Field Guide](/resources/06-fifteen-micron-boundary/) Moxi GO II Moxi V Moxi Z ### The 15-Micrometer Decision: A Practical Cassette Selection Framework The 15 μm boundary provides clear selection criterion: cells under 15 micrometers use S+ cassettes, cells over 15 micrometers use M+ cassettes. This boundary isn't arbitrary - it's where each aperture size achieves the optimal 15-40% cell-to-aperture ratio for signal quality and sizing resolution. Know your cell size, follow the boundary, and cassette selection becomes automatic. [Read Field Guide](/resources/06-fifteen-micron-boundary/) [Field Guide](/resources/06-physics-vs-algorithms/) ### Physics vs Algorithms Every AI-based image counter was trained on a specific dataset, learning to recognize "cell" and "not cell" from images someone curated. When your sample doesn't match that training set, physics-based counting tells a more reliable story. [Read Field Guide](/resources/06-physics-vs-algorithms/) [Field Guide](/resources/06-singulator-integration-workflow/) ### Singulator Integration Workflow: Your Sous Chef for Automated Tissue Dissociation The Precision Cell Systems Singulator provides automated, standardized tissue dissociation. But automation doesn't mean zero debris or guaranteed sample quality—integrating a Moxi QC checkpoint is what makes the workflow dependable. [Read Field Guide](/resources/06-singulator-integration-workflow/) [Field Guide](/resources/07-preloading-qc-checkpoint/) ### Preloading QC Checkpoints Single-cell genomics workflows have a critical decision point: do you load this sample onto an expensive chip, or does it need more cleanup first? A preloading QC checkpoint answers that with confidence. [Read Field Guide](/resources/07-preloading-qc-checkpoint/) [Field Guide](/resources/07-til-immune-killing-optimization/) Moxi GO II Moxi V Moxi Z ### TIL Counting and Immune Cell Killing: Dual-Cassette Optimization Guide TIL counting and immune cell killing assays are immediate applications for dual-cassette workflows. Cancer cells are large, T cells are small - no single cassette optimizes both. Run S+ for accurate T cell counts, M+ for accurate tumor/target counts. The extra run takes minutes but delivers publication-quality E:T ratios and killing percentages. [Read Field Guide](/resources/07-til-immune-killing-optimization/) [Field Guide](/resources/07-training-new-users/) Moxi GO II Moxi V ### Training New Users: Why Pre-Optimized Reagents Simplify Onboarding New lab members need to generate valid data quickly. Teaching protocol optimization takes weeks. Teaching protocol execution takes minutes. The user manual is designed to be super easy - put X amount of viability reagent, put X amount of sample, incubate and go. When reagents are pre-optimized, training focuses on execution, not development. [Read Field Guide](/resources/07-training-new-users/) [Field Guide](/resources/01-small-cell-weak-signal/) Moxi GO II Moxi V Moxi Z ### The Small Cell Weak Signal Problem: Why Your Lymphocyte Counts May Be Wrong Small cells measured through oversized apertures generate weak electrical signals that fall below detection thresholds or get confused with debris. If you're counting lymphocytes, PBMCs, Jurkat cells, or any suspension lines under 15 micrometers with the wrong cassette, you're likely undercounting. Switch to S+ cassettes where the smaller aperture ensures your small cells generate strong, detectable signals clearly distinguishable from noise. [Read Field Guide](/resources/01-small-cell-weak-signal/) [Field Guide](/resources/02-large-cell-clog-risk/) Moxi GO II Moxi V Moxi Z ### The Large Cell Clog Risk: Preventing Measurement Interruptions Large cells approaching the aperture diameter create artificially high signals and risk clogging the sensing orifice. Clogging interrupts runs, wastes samples, and requires cassette replacement mid-experiment. For adherent cell lines like CHO, HEK293, and HeLa, and for primary tissue cells over 15 micrometers, M+ cassettes provide the larger aperture necessary to prevent physical blockage. [Read Field Guide](/resources/02-large-cell-clog-risk/) [Field Guide](/resources/03-mixed-population-dilemma/) Moxi GO II Moxi V Moxi Z ### The Mixed Population Dilemma: When One Cassette Can't Capture Everything When your sample contains both small and large cells, no single cassette optimizes measurement for both populations. The solution: run the same sample twice - once with S+ to get accurate small cell counts, once with M+ to get accurate large cell counts. This dual-cassette workflow delivers accurate data for both populations rather than compromised data for everyone. [Read Field Guide](/resources/03-mixed-population-dilemma/) [Field Guide](/resources/04-coincidence-artifact/) Moxi GO II Moxi V Moxi Z ### The Coincidence Artifact: When Two Cells Count as One Coincidence - multiple cells in the aperture simultaneously - causes two cells to be counted as one, corrupting both count and size data. Optimal aperture utilization means targeting 15-40% of aperture diameter so cells generate strong signals while avoiding coincidence artifacts. Match your cassette to your cell size, stay within concentration guidelines, and coincidence becomes a non-issue. [Read Field Guide](/resources/04-coincidence-artifact/) [Field Guide](/resources/brain-tissue-complexity-myelin-lipids-neuronal-nuclei/) Singulator 200+ ### Overcoming Brain Tissue Complexity: Myelin, Lipids, and Fragile Neuronal Nuclei Brain FFPE tissue creates unique nuclei isolation challenges. Myelin debris, lipid contamination, and fragile neuronal nuclei require controlled automated processing to preserve cell-type diversity for single-nucleus sequencing. [Read Field Guide](/resources/brain-tissue-complexity-myelin-lipids-neuronal-nuclei/) [Field Guide](/resources/brain-tumor-ffpe-surgical-resection-single-cell/) Singulator 200+ ### Brain Tumor FFPE Processing: From Surgical Resection to Single-Nucleus Insights Process brain tumor FFPE from surgical resections on the Singulator 200+. Preserve cancer cells and immune populations for snRNA-seq and spatial analysis. [Read Field Guide](/resources/brain-tumor-ffpe-surgical-resection-single-cell/) [Field Guide](/resources/ffpe-neurodegenerative-disease-research-singulator/) Singulator 200+ ### FFPE Nuclei Extraction for Neurodegenerative Disease Research Extract nuclei from FFPE brain tissue for Alzheimer's, Parkinson's, and Lewy body research. Longitudinal cohorts, cell-type preservation, and disease staging on the Singulator 200+. [Read Field Guide](/resources/ffpe-neurodegenerative-disease-research-singulator/) [Field Guide](/resources/integrating-snrna-seq-spatial-transcriptomics-brain-ffpe/) Singulator 200+ ### Integrating snRNA-seq with spatial transcriptomics for brain mapping Pair spatial transcriptomics with snRNA-seq from the same FFPE brain block. Block allocation, platform selection, and nuclei quality for multi-omic brain studies. [Read Field Guide](/resources/integrating-snrna-seq-spatial-transcriptomics-brain-ffpe/) [Field Guide](/resources/maximizing-limited-brain-tissue-sections-ffpe/) Singulator 200+ ### Maximizing Results from Limited Brain Tissue Sections Get high-quality nuclei from limited postmortem brain FFPE sections. Process NIH biobank allocations, hospital archives, and surgical specimens on the Singulator 200+. [Read Field Guide](/resources/maximizing-limited-brain-tissue-sections-ffpe/) [Field Guide](/resources/navigating-postmortem-brain-tissue-ffpe-genomics/) Singulator 200+ ### Navigating postmortem brain tissue for FFPE genomics Practical guide to postmortem brain FFPE challenges: necropsy timing, fixation variability, biobank sourcing, myelin debris, and how the Singulator 200+ standardizes nuclei extraction. [Read Field Guide](/resources/navigating-postmortem-brain-tissue-ffpe-genomics/) [Field Guide](/resources/reproducible-multi-site-brain-tissue-atlases-singulator/) Singulator 200+ ### Building Reproducible Multi-Site Brain Tissue Atlases Standardize brain FFPE nuclei extraction across consortium sites with the Singulator 200+. Eliminate operator variability, prevent batch effects, and scale for atlas projects. [Read Field Guide](/resources/reproducible-multi-site-brain-tissue-atlases-singulator/) [Field Guide](/resources/complete-ffpe-workflow-archive-to-publication-singulator/) Singulator 200+ ### Complete FFPE workflow: from archive to publication with the Singulator 200+ End-to-end protocol walkthrough from FFPE block selection through deparaffinization, nuclei isolation, quality control, library preparation, sequencing, and data analysis using the Singulator 200+. [Read Field Guide](/resources/complete-ffpe-workflow-archive-to-publication-singulator/) [Field Guide](/resources/deparaffinization-rehydration-singulator-200-plus-green-cartridge/) Singulator 200+ ### Deparaffinization Rehydration Optimization How the Singulator 200+ GREEN cartridge automates FFPE deparaffinization and rehydration, eliminating toxic solvents, fume hoods, and manual ethanol series from nuclei extraction workflows. [Read Field Guide](/resources/deparaffinization-rehydration-singulator-200-plus-green-cartridge/) [Field Guide](/resources/ffpe-downstream-platform-compatibility/) Singulator 200+ ### FFPE Downstream Platform Compatibility Practical guide to connecting Singulator 200+ FFPE nuclei with downstream analysis platforms including 10x Chromium Flex, Xenium, ATAC-seq, Visium, and MERFISH, covering quality requirements, expected yields, and multi-platform study design. [Read Field Guide](/resources/ffpe-downstream-platform-compatibility/) [Field Guide](/resources/ffpe-input-preparation-optimizing-curl-thickness-tissue-mass-block-age-singulator-200-plus/) Singulator 200+ ### FFPE Input Preparation Practical guide to preparing FFPE tissue inputs for the Singulator 200+ automated nuclei extraction platform, covering curl thickness selection, tissue mass requirements, block age effects, quality assessment, and handling difficult or precious specimens. [Read Field Guide](/resources/ffpe-input-preparation-optimizing-curl-thickness-tissue-mass-block-age-singulator-200-plus/) [Field Guide](/resources/ffpe-troubleshooting-guide-singulator-200-plus/) Singulator 200+ ### FFPE Troubleshooting Guide: Diagnosing and Resolving Common Singulator 200+ Issues Practical troubleshooting guide for the Singulator 200+ FFPE nuclei extraction workflow, covering the five most common problem categories: low yield, excessive debris, poor RNA quality, batch-to-batch variability, and cartridge/instrument errors. [Read Field Guide](/resources/ffpe-troubleshooting-guide-singulator-200-plus/) [Field Guide](/resources/minimal-precious-ffpe-samples-singulator-200-plus/) Singulator 200+ ### Working with Minimal and Precious FFPE Samples Practical strategies for maximizing nuclei recovery from limited FFPE tissue on the Singulator 200+, covering block quality assessment, sectioning waste reduction, the pilot curl approach for irreplaceable specimens, handling needle biopsies and crumbly blocks, and preserving nuclei yield post-processing. [Read Field Guide](/resources/minimal-precious-ffpe-samples-singulator-200-plus/) [Field Guide](/resources/nuclei-isolation-quality-assessment-yield-viability-dv200-ffpe-singulator/) Singulator 200+ ### FFPE Nuclei Isolation Quality Assessment Quality assessment of nuclei isolated from FFPE tissue using the Singulator 200+, covering yield measurement, DAPI staining for morphology, DV200 RNA quality metrics, erythrocyte contamination assessment, and structured go/no-go decision frameworks before downstream sequencing. [Read Field Guide](/resources/nuclei-isolation-quality-assessment-yield-viability-dv200-ffpe-singulator/) [Field Guide](/resources/02-ai-segmentation-failures/) ### AI Segmentation Failures AI segmentation algorithms fail when encountering debris, clusters, or samples they were not trained on—resulting in minimum 3-4% error per image even under. [Read Field Guide](/resources/02-ai-segmentation-failures/) [Field Guide](/resources/07-single-cell-loading-decision/) ### Single-Cell Loading Decision Framework: Confident Go/No-Go Before Chip Commitment Every single-cell experiment represents a significant investment—consumables alone cost $500–1000+ per chip, plus downstream sequencing—so a confident go/no-go decision before chip commitment protects the run. [Read Field Guide](/resources/07-single-cell-loading-decision/) No resources match your current filters. Clear All Filters ## Explore More Topics [### Application Notes](/resources/collections/application-notes/)[### Blog & Insights](/resources/collections/blog-insights/)[### Cell & Gene Therapy Resources](/resources/collections/cell-gene-therapy/) ## Have a question about this topic? Our scientific team can help you match the right instrument and workflow to your research. [Contact Us](https://precisioncellsystems.com/contact/)