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Automated and standardized colony counting for the hematopoietic colony-forming unit (CFU) assay

Now Available: ³§°Õ·¡²Ñ±¹¾±²õ¾±´Ç²Ôâ„¢ 21 CFR Part 11 Compliance Software Add-On (Catalog #500-0110). Request pricing above for more information.

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Automated and standardized colony counting for the hematopoietic colony-forming unit (CFU) assay

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Automated and standardized colony counting for the hematopoietic colony-forming unit (CFU) assay
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Products for Your Protocol
To see all required products for your protocol, please consult the Protocols and Documentation.

What Our Product Engineer Says

We developed ³§°Õ·¡²Ñ±¹¾±²õ¾±´Ç²Ôâ„¢ as our own "expert CFU counter in a box" and to remove some of the subjectivity inherent in counting colonies in a CFU assay. Using standardized algorithms helps to reduce variations that might be seen when different people are counting and scoring colonies manually.

Oliver EgelerSenior Systems Engineer
Oliver Egeler, Senior Systems Engineer

Overview

³§°Õ·¡²Ñ±¹¾±²õ¾±´Ç²Ôâ„¢ consists of an instrument and software designed specifically for imaging and counting colonies in hematopoietic colony-forming unit (CFU) assays using MethoCultâ„¢ media and meniscus-free ³§³¾²¹°ù³Ù¶Ù¾±²õ³óâ„¢ cultureware. ³§°Õ·¡²Ñ±¹¾±²õ¾±´Ç²Ôâ„¢ software, known as Analysis Packages, replaces the need to manually count colonies using a microscope. With the addition of the ³§°Õ·¡²Ñ±¹¾±²õ¾±´Ç²Ôâ„¢ 21 CFR Part 11 Compliance Software Add-On (Catalog #500-0110), ³§°Õ·¡²Ñ±¹¾±²õ¾±´Ç²Ôâ„¢ can support workflows consistent with FDA Title 21 CFR Part 11 regulations on electronic records.

For human cultures, three Analysis Packages have been designed for scoring and counting hematopoietic colonies produced by erythroid, myeloid and multi-potential progenitor cells in 14-day assays of CB, BM and MPB cultured in MethoCultâ„¢ Optimum media. A fourth Analysis Package is also available for counting the total number of colonies in 7-day assays of CB cultured in MethoCultâ„¢ Express medium.

For mouse BM cultures, three Analysis Packages have been designed to count total numbers of hematopoietic colonies produced by all combined myeloid and erythroid progenitors in M3434, myeloid progenitors only in M3534 and erythroid progenitors only in M3436.

Selection of at least one Analysis Package is required for each instrument purchase. Additional Analysis Packages and software add-ons to support 21 CFR Part 11 compliance are sold separately. Select your preferred Analysis Package and select Request Pricing for further information. Several purchase and leasing options are available.

For more information about Instrument Services including additional service packages and installation software please see our instrumentation overview.

Browse our Frequently Asked Questions (FAQs) on performing the CFU assay and explore its utility as part of the cell therapy workflow.
Application
Colony Assay, Functional Assay, Genome Editing
Brand
STEMvision
Area of Interest
Cord Blood Banking, Stem Cell Biology, Transplantation Research, Cell Therapy Development

Data Figures

Representative STEMvision™ Images Showing Colonies Derived from CB Progenitors after 7 Days of Culture in MethoCult™ Express, and from CB, BM and MPB after 14 Days of Culture in MethoCult™ Optimum

Figure 1. Representative STEMvision™ Images Showing Colonies Derived from CB Progenitors after 7 Days of Culture in MethoCult™ Express, and from CB, BM and MPB after 14 Days of Culture in MethoCult™ Optimum

These images have been analyzed by STEMvision™ Human (A) 7-Day and (B-D) 14-Day Analysis Packages. Green circles identify individual colonies in a 7-day CB CFU assay that scores total CFUs only (A). Orange and red circles identify erythroid colonies, yellow circles identify myeloid colonies and blue circles identify mixed colonies in 14-day CB (B), BM (C) and MPB (D) CFU assays. Erythroid and mixed colonies that contain hemoglobinized cells are shown in true red color.

STEMvision™ Automated Counting of Total, Erythroid (BFU-E) and Myeloid (CFU-G/M/GM) Colonies Is Highly Correlated to Manual Counts of 14-Day CB CFU Assays

Figure 2. STEMvision™ Automated Counting of Total, Erythroid (BFU-E) and Myeloid (CFU-G/M/GM) Colonies Is Highly Correlated to Manual Counts of 14-Day CB CFU Assays

Cryopreserved CB cells were thawed, plated in MethoCult™ Optimum and cultured for 14 days. The resulting colonies were then counted both manually using an inverted microscope, and automatically using STEMvision™ with the Human CB 14-Day CFU Analysis Package (Catalog #22005). Gray dashed lines represent a perfect linear correlation between manual and automated counts. Red solid lines represent the actual linear correlation between manual and automated counts. The mathematical equations and correlation coefficients (R2) that describe each data set (n=130 CFU assays) are as follows: A: y=1.02x + 1.39, R2=0.96 for Total Colonies, B: y=1.05x + 1.53, R2=0.89 for BFU-E, C: y=0.99x + 0.13, R2=0.94 for CFU-G/M/GM.

STEMvision™ Automated Counting of Mixed Colonies Falls Within the Range of Manual Counts of 14-Day CB CFU Assays

Figure 3. STEMvision™ Automated Counting of Mixed Colonies Falls Within the Range of Manual Counts of 14-Day CB CFU Assays

Thirty individual 14-day CB CFU assays were counted by three to seven people. The numbers of mixed colonies (CFU-GEMM) colonies counted manually in each well are shown by the black open circles (n=80 total assay scores). Manual CFU-GEMM counts in most cultures varied significantly between individual people. STEMvision™ counts of the same cultures (red circles) provided a CFU-GEMM count that was typically within the range of manual counts.

STEMvision™ Automated Scoring of Total, Erythroid (BFU-E + CFU-E) and Myeloid (CFU-G/M/GM) Colonies Is Highly Correlated to Manual Counts of 14-Day BM CFU Assays

Figure 4. STEMvision™ Automated Scoring of Total, Erythroid (BFU-E + CFU-E) and Myeloid (CFU-G/M/GM) Colonies Is Highly Correlated to Manual Counts of 14-Day BM CFU Assays

Cryopreserved BM cells were thawed, plated in MethoCult™ Optimum, cultured for 14 days, and the resulting colonies then scored both manually using an inverted microscope and automatically using STEMvision™ with the Human BM 14-Day CFU Analysis Package (Catalog #22006). The BM Analysis Package can identify and count erythroid colonies produced by CFU-E and BFU-E separately, but these are combined in panel B. Gray dashed lines represent a perfect linear correlation between manual and automated counts. Red solid lines represent the actual linear correlation between manual and automated counts. The mathematical equations and correlation coefficients (R2) that describe each data set (n=120 CFU assays) are as follows: A: y=0.88x + 8.79, R2=0.95 for Total Colonies, B: y=0.83x + 6.71, R2=0.89 for CFU-E + BFU-E, C: y=0.92x + 2.55, R2=0.94 for CFU-G/M/GM.

STEMvision™ Automated Counting of Mixed Colonies Falls Within the Range of Manual Counts of 14-Day BM CFU Assays

Figure 5. STEMvision™ Automated Counting of Mixed Colonies Falls Within the Range of Manual Counts of 14-Day BM CFU Assays

Thirty individual 14-day BM CFU assays were counted by three to seven people. The numbers of mixed (CFU-GEMM) colonies counted manually in each well is shown by the black open circles (n=82 total assay scores). Manual CFU-GEMM counts in most cultures varied significantly between individual people. STEMvision™ counts of the same cultures (red circles) provided a CFU-GEMM count that was typically within the range of manual counts.

STEMvision™ Automated Counting of Total, Erythroid (BFU-E) and Myeloid (CFU-G/M/GM) Colonies Is Highly Correlated to Manual Counts of 14-Day MPB CFU Assays

Figure 6. STEMvision™ Automated Counting of Total, Erythroid (BFU-E) and Myeloid (CFU-G/M/GM) Colonies Is Highly Correlated to Manual Counts of 14-Day MPB CFU Assays

Cryopreserved MPB cells were thawed, plated in MethoCult™ Optimum, cultured for 14 days, and the resulting colonies then scored both manually using an inverted microscope and automatically using STEMvision™ with the Human MPB 14-Day CFU Analysis Package (Catalog #22007). Gray dashed lines represent a perfect linear correlation between manual and automated counts. Red solid lines represent the actual linear correlation between manual and automated counts. The mathematical equations and correlation coefficients (R2) that describe each data set (n=143 CFU assays) are as follows: A: y=0.97x + 2.44, R2=0.97 for Total Colonies, B: y=0.96x + 3.74, R2=0.91 for BFU-E, C: y=0.96x + 0.90, R2=0.95 for CFU-G/M/GM.

STEMvision™ Automated Scoring of Mixed Colonies Falls Within the Range of Manual Counts of 14-Day MPB CFU Assays

Figure 7. STEMvision™ Automated Scoring of Mixed Colonies Falls Within the Range of Manual Counts of 14-Day MPB CFU Assays

Thirty individual 14-day MPB CFU assays were counted by three to seven people. The numbers of mixed (CFU-GEMM) colonies counted manually in each well is shown by the black open circles (n=82 total assay scores). Manual CFU-GEMM counts in most cultures varied significantly between individual people. STEMvision™ counts of the same cultures (red circles) provided a CFU-GEMM count that was typically within the range of manual counts.

Representative STEMvision™ Images Showing Colonies Derived from Mouse BM Progenitors After 12 Days of Culture in MethoCult™ GF M3434, MethoCult™ GF M3534 or MethoCult™ SF M3436 Media

Figure 8. Representative STEMvision™ Images Showing Colonies Derived from Mouse BM Progenitors After 12 Days of Culture in MethoCult™ GF M3434, MethoCult™ GF M3534 or MethoCult™ SF M3436 Media

Images of mouse BM cells cultured in (A) MethoCult™ GF M3434, (B) MethoCult™ GF M3534 and (C) MethoCult™ SF M3436 were acquired using STEMvision™. The corresponding STEMvision™ Mouse Analysis Package (Table 1) was used to analyze each image. Red circles identify the smallest colonies - size class 1, yellow circles - size class 2, blue circles - size class 3 and orange circles identify the largest colonies - size class 4.

STEMvision™ Automated Counting is Highly Correlated to Manual Counting of Total (Myeloid Plus Erythroid) Colonies in Mouse BM CFU Assays

Figure 9. STEMvision™ Automated Counting is Highly Correlated to Manual Counting of Total (Myeloid Plus Erythroid) Colonies in Mouse BM CFU Assays

BM cells were plated in MethoCult™ GF M3434 (Catalog #03434/03444). Colonies were counted on days (A) 7, (B) 10 and (C) 12 both manually using an inverted microscope, and automatically using STEMvision™ equipped with the Mouse Total CFU Analysis Package (Catalog #22008). We recommend counting CFU assays of mouse progenitor cells plated in M3434 between 10 and 12 days. Gray dashed lines represent a theoretical perfect linear correlation between manual and automated counts. Red solid lines represent the actual linear correlation between manual and automated counts. The slope, 95% confidence intervals, correlation coefficients (R2) and sample size for each data set are provided in Table 1.

STEMvision™ Automated Counting is Highly Correlated to Manual Counting of Myeloid Colonies in Mouse BM CFU Assays

Figure 10. STEMvision™ Automated Counting is Highly Correlated to Manual Counting of Myeloid Colonies in Mouse BM CFU Assays

BM cells were plated in MethoCult™ GF M3534 (Catalog #03534). Colonies were counted on days (A) 7, (B) 10 and (C) 12 both manually using an inverted microscope, and automatically using STEMvision™ equipped with the Mouse Myeloid CFU Analysis Package (Catalog #22009). We recommend counting CFU assays of mouse myeloid progenitor cells plated in M3534 between 10 and 12 days. Gray dashed lines represent a theoretical perfect linear correlation between manual and automated counts. Red solid lines represent the actual linear correlation between manual and automated counts. The slope, 95% confidence intervals, correlation coefficients (R2) and sample size for each data set are provided in Table 1.

STEMvision™ Automated Counting is Highly Correlated to Manual Counting of Erythroid Colonies in Mouse BM CFU Assays

Figure 11. STEMvision™ Automated Counting is Highly Correlated to Manual Counting of Erythroid Colonies in Mouse BM CFU Assays

BM cells were plated in MethoCult™ SF M3436 (Catalog #03436). Colonies were counted on days (A) 7, (B) 10 and (C) 12 - 14 both manually using an inverted microscope, and automatically using STEMvision™ equipped with the Mouse Erythroid CFU Analysis Package (Catalog #22011). We recommend counting CFU assays of mouse erythroid progenitor cells plated in M3436 between of 10 to 14 days. Gray dashed lines represent a theoretical perfect linear correlation between manual and automated counts. Red solid lines represent the actual linear correlation between manual and automated counts. The slope, 95% confidence intervals, correlation coefficients (R2) and sample size for each data set are provided in Table 1.

Table 1. Correlation Between Automated STEMvision™ and Manual Colony Counting

Table 1. Correlation Between Automated STEMvision™ and Manual Colony Counting

*CI: Confidence Internal
**Mouse CFU assays of erythroid progenitor cells plated in M3436 should be counted between 10 to 14 days.

Protocols and Documentation

Find supporting information and directions for use in the Product Information Sheet or explore additional protocols below.

Document Type
Product Name
Catalog #
Lot #
Language
Document Type
Product Name
Catalog #
22000
Lot #
All
Language
English

Applications

This product is designed for use in the following research area(s) as part of the highlighted workflow stage(s). Explore these workflows to learn more about the other products we offer to support each research area.

Resources and Publications

Publications (21)

FSL-1 Pre-Administration Protects Radiation-Induced Hematopoietic Organs Through the Modulation of the TLR Signaling Pathway V. R. Dronamraju et al. International Journal of Molecular Sciences 2025 May

Abstract

Substantial progress has been made in the development of radiation countermeasures, resulting in the recent approval of several mitigators; however, there has yet to be an approved prophylactic radioprotectant. Research on countermeasure performance in mixed neutron and gamma radiation fields has also been scarce. Fibroblast-stimulating lipopeptide (FSL-1) is a novel synthetic agonist for toll-like receptor 2/6. In previous studies, the administration of FSL-1 before and after gamma radiation significantly improved survival outcomes for mice through the activation of the NF-κB pathway. In the current study, we tested FSL-1’s radioprotective abilities in a mixed radiation field that models one produced by a nuclear detonation in 11–14-week-old C57BL/6 male and female mice. We demonstrate that a single dose of 1.5 mg/kg of FSL-1 administered 12 h prior to 65% neutron 35% gamma mixed-field (MF) irradiation enhances survival, accelerates recovery of hematopoietic cell and stem cell populations, reduces inflammation, and protects innate immune function in mice. FSL-1’s ability to recover blood and protect immune functions is important in countering the high rate of incidence of sepsis caused by MF radiation’s damaging effects. These results demonstrate that FSL-1 is a promising prophylactic countermeasure where exposure to MF radiation is anticipated.
Characterization of E1 enzyme dependencies in mutant- UBA1 human cells reveals UBA6 as a novel therapeutic target in VEXAS syndrome C. A. Clough et al. Leukemia 2025 Jun

Abstract

VEXAS syndrome is a clonal hematopoietic disorder characterized by hyperinflammation, bone marrow failure, and high mortality. The molecular hallmark of VEXAS is somatic mutations at methionine 41 (M41) in the E1 ubiquitin enzyme, UBA1. These mutations induce a protein isoform switch, but the mechanisms underlying disease pathogenesis remain unclear. Here, we developed a human cell model of VEXAS syndrome by engineering the male monocytic THP1 cell line to express the common UBA1 M41V mutation. We found that mutant UBA1 M41V cells exhibit aberrant UBA1 isoform expression, increased vacuolization, and upregulation of the unfolded protein response, recapitulating key features of VEXAS. Moreover, proteomic analyses revealed dysregulated ubiquitination and proteotoxic stress in UBA1 M41V cells, with alterations in inflammatory and stress-response pathways. Functional studies demonstrated that UBA1 M41V cells were highly sensitive to genetic or pharmacological inhibition of E1 ubiquitin enzymes. Treatment with the E1 enzyme inhibitor TAK-243 preferentially suppressed colony formation of UBA1 M41V cells as compared to WT cells. Moreover, UBA1 M41V cells exhibited greater sensitivity to TAK-243 in competition assays and showed increased apoptosis. Interestingly, TAK-243 preferentially inhibited UBA6 activity over UBA1, suggesting that UBA6 may compensate for UBA1 dysfunction in UBA1 M41V cells. Targeting UBA6 using shRNA or the UBA6-specific inhibitor phytic acid further revealed an acquired dependency on UBA6 in UBA1 M41V cells. Phytic acid selectively impaired growth and colony formation in UBA1 M41V cells while sparing WT cells, highlighting a potential therapeutic vulnerability. Together, these findings establish a novel human model of VEXAS syndrome, identify key roles for UBA1 and UBA6 in disease pathogenesis, and demonstrate that UBA6 inhibition represents a promising therapeutic strategy for selectively targeting UBA1 mutant clones. Subject terms: Haematological cancer, Cell signalling
High frequency CCR5 editing in human hematopoietic stem progenitor cells protects xenograft mice from HIV infection D. T. Claiborne et al. Nature Communications 2025 Jan

Abstract

The only cure of HIV has been achieved in a small number of people who received a hematopoietic stem cell transplant (HSCT) comprising allogeneic cells carrying a rare, naturally occurring, homozygous deletion in the CCR5 gene. The rarity of the mutation and the significant morbidity and mortality of such allogeneic transplants precludes widespread adoption of this HIV cure. Here, we show the application of CRISPR/Cas9 to achieve >90% CCR5 editing in human, mobilized hematopoietic stem progenitor cells (HSPC), resulting in a transplant that undergoes normal hematopoiesis, produces CCR5 null T cells, and renders xenograft mice refractory to HIV infection. Titration studies transplanting decreasing frequencies of CCR5 edited HSPCs demonstrate that <90% CCR5 editing confers decreasing protective benefit that becomes negligible between 54% and 26%. Our study demonstrates the feasibility of using CRISPR/Cas9/RNP to produce an HSPC transplant with high frequency CCR5 editing that is refractory to HIV replication. These results raise the potential of using CRISPR/Cas9 to produce a curative autologous HSCT and bring us closer to the development of a cure for HIV infection. Subject terms: HIV infections, CRISPR-Cas9 genome editing, Retrovirus, Translational research
Now Available: ³§°Õ·¡²Ñ±¹¾±²õ¾±´Ç²Ôâ„¢ 21 CFR Part 11 Compliance Software Add-On (Catalog #500-0110). Request pricing above for more information.