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Hands-off to Organoid Assays! To be manual or not to be manual—that is the question!

  • Writer: Advanced Solutions
    Advanced Solutions
  • Oct 13, 2025
  • 3 min read

Updated: Dec 17, 2025

As funding and regulatory agencies emphasize human-relevant model systems and new approach methodologies (NAMs), the use of organoid culture is skyrocketing in the research community. Many groups are asking, "How can I improve the use of organoid culture systems to provide more predictive human data?" Most hurdles stem from the variability that arises through manual operations and workflows.


Common Pitfalls in Manual Organoid Work


Here are five common pitfalls when conducting organoid work manually:


1. Inconsistent Pipetting

Inconsistent pipetting can occur from person to person, day to day, or even hour to hour. This inconsistency can lead to differences in how cells, compounds, and organoids are deposited across experimental or assay conditions. Ultimately, this variability results in inconsistent assay results and readouts.


2. Organoid Fragmentation and Integrity Loss

Manual pipetting can cause organoid fragmentation due to variable aspirating and dispensing shearing. This leads to variable organoid numbers (as fragments) per well in a culture or assay. Such heterogeneity contributes to data variability and reduces organoid performance.


3. Time-Consuming Compound Addition and Media Exchanges

Like any multi-well plate assay, compound additions and media exchanges can be time-consuming. Different assays may require inconvenient timing for these changes, adding to the workload.


4. Limited Scaling

The time-intensive nature of ensuring consistent pipetting, preventing organoid fragmentation, and conducting compound additions and media exchanges limits the scalability of organoid studies when performed manually.


5. Quality Control Challenges

Inconsistencies from manual processing make it difficult to ensure quality control practices. This inefficiency can hinder reliable and efficient quality control.


How to Avoid These Pitfalls


So, how can you avoid these pitfalls? The answer lies in conducting organoid assays using automated solutions and technologies.


How BioAssemblyBot® Platforms Solve Organoid Challenges


1. Consistent Pipetting

Robotic technologies are programmed to pipette prescribed volumes consistently. This eliminates the risk of inconsistency in cell number, media volume, or compound concentration. Our robotic systems, or BABs, are paired with user-friendly software called BioApps. This allows users to program volumes, movement paths, and deposition speeds easily.



2. Maintaining Organoid Integrity

With precise pipetting control, robotic systems minimize organoid fragmentation or shearing. This ensures consistent organoid culture numbers per well and maintains the integrity of the organoid cultures. This is invaluable for those working with unique patient-derived samples or iPSC-derived organoids. Our in-house team of 3D biology experts has validated the settings required for optimal organoid deposition, saving researchers time and materials.



3. Time Savings for Compound Addition and Media Exchanges

Robotic systems can conduct all necessary compound additions and media exchanges precisely, day or night. This frees up researchers to focus on other essential tasks while saving money on reagents by reducing waste. Our BioApps software can be easily modified based on each assay’s unique scheme.


4. Scale-Up Capabilities

Reproducibility and precision from robotics enable scale-up, both in terms of the types of multi-well plates and the quantity of plates. Our BABs can integrate seamlessly into existing infrastructure, further enabling scale.



5. Quality Control Integration

Automation platforms integrated with quality control systems and programmed through integrated software enable decision points based on data output. This saves time and reduces the costly materials required to run organoid assays.


Why Choose Advanced Solutions?



Advanced Solutions is uniquely positioned to enable the automation of organoid assay work. We provide bundled solutions tailored to the needs of scientists and researchers working with organoids.


Our platforms save time by eliminating the need to program systems from scratch for various tasks related to common practices and workflows in organoid work. Our expert team is ready to help integrate our technologies into your current workflows without causing disruption. This enables the removal of pitfalls without reinventing the wheel.


Contact us to explore how we can help you experience the benefits of organoid automation!



The Future of Organoid Research


The future of organoid research is bright! As we continue to refine our technologies, we empower researchers and clinicians to make groundbreaking advancements in regenerative medicine and drug discovery. The shift from manual to automated systems is not just a trend; it’s a revolution in how we approach organoid culture.


Embracing Automation


Embracing automation in organoid assays is essential for enhancing reproducibility and reliability. By reducing human error and variability, we can focus on what truly matters: making significant strides in healthcare and life sciences.


Conclusion


In conclusion, transitioning to automated organoid assays is a game-changer. It allows researchers to overcome common pitfalls associated with manual processes. With the right tools and technologies, we can unlock the full potential of organoid cultures, paving the way for innovative breakthroughs in medicine.


Let’s embrace the future together!

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