Altair-LSFM: A High-Resolution, Easy-to-Build Light-Sheet Microscope for Sub-Cellular Imaging

  1. Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, United States
  2. Cecil H. and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, United States
  3. Department of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland

Peer review process

Not revised: This Reviewed Preprint includes the authors’ original preprint (without revision), an eLife assessment, public reviews, and a provisional response from the authors.

Read more about eLife’s peer review process.

Editors

  • Reviewing Editor
    Felix Campelo
    Institute of Photonic Sciences, Barcelona, Spain
  • Senior Editor
    Felix Campelo
    Institute of Photonic Sciences, Barcelona, Spain

Reviewer #1 (Public review):

Summary:

The article presents the details of the high-resolution light-sheet microscopy system developed by the group. In addition to presenting the technical details of the system, its resolution has been characterized and its functionality demonstrated by visualizing subcellular structures in a biological sample.

Strengths:

(1) The article includes extensive supplementary material that complements the information in the main article.

(2) However, in some sections, the information provided is somewhat superficial.

Weaknesses:

(1) Although a comparison is made with other light-sheet microscopy systems, the presented system does not represent a significant advance over existing systems. It uses high numerical aperture objectives and Gaussian beams, achieving resolution close to theoretical after deconvolution. The main advantage of the presented system is its ease of construction, thanks to the design of a perforated base plate.

(2) Using similar objectives (Nikon 25x and Thorlabs 20x), the results obtained are similar to those of the LLSM system (using a Gaussian beam without laser modulation). However, the article does not mention the difficulties of mounting the sample in the implemented configuration.

(3) The authors present a low-cost, open-source system. Although they provide open source code for the software (navigate), the use of proprietary electronics (ASI, NI, etc.) makes the system relatively expensive. Its low cost is not justified.

(4) The fibroblast images provided are of exceptional quality. However, these are fixed samples. The system lacks the necessary elements for monitoring cells in vivo, such as temperature or pH control.

Reviewer #2 (Public review):

Summary:

The authors present Altair-LSFM (Light Sheet Fluorescence Microscope), a high-resolution, open-source microscope, that is relatively easy to align and construct and achieves sub-cellular resolution. The authors developed this microscope to fill a perceived need that current open-source systems are primarily designed for large specimens and lack sub-cellular resolution or are difficult to construct and align, and are not stable. While commercial alternatives exist that offer sub-cellular resolution, they are expensive. The authors' manuscript centers around comparisons to the highly successful lattice light-sheet microscope, including the choice of detection and excitation objectives. The authors thus claim that there remains a critical need for high-resolution, economical, and easy-to-implement LSFM systems.

Strengths:

The authors succeed in their goals of implementing a relatively low-cost (~ USD 150K) open-source microscope that is easy to align. The ease of alignment rests on using custom-designed baseplates with dowel pins for precise positioning of optics based on computer analysis of opto-mechanical tolerances, as well as the optical path design. They simplify the excitation optics over Lattice light-sheet microscopes by using a Gaussian beam for illumination while maintaining lateral and axial resolutions of 235 and 350 nm across a 260-um field of view after deconvolution. In doing so they rest on foundational principles of optical microscopy that what matters for lateral resolution is the numerical aperture of the detection objective and proper sampling of the image field on to the detection, and the axial resolution depends on the thickness of the light-sheet when it is thinner than the depth of field of the detection objective. This concept has unfortunately not been completely clear to users of high-resolution light-sheet microscopes and is thus a valuable demonstration. The microscope is controlled by an open-source software, Navigate, developed by the authors, and it is thus foreseeable that different versions of this system could be implemented depending on experimental needs while maintaining easy alignment and low cost. They demonstrate system performance successfully by characterizing their sheet, point-spread function, and visualization of sub-cellular structures in mammalian cells, including microtubules, actin filaments, nuclei, and the Golgi apparatus.

Weaknesses:

There is a fixation on comparison to the first-generation lattice light-sheet microscope, which has evolved significantly since then:

(1) The authors claim that commercial lattice light-sheet microscopes (LLSM) are "complex, expensive, and alignment intensive", I believe this sentence applies to the open-source version of LLSM, which was made available for wide dissemination. Since then, a commercial solution has been provided by 3i, which is now being used in multiple cores and labs but does require routine alignments. However, Zeiss has also released a commercial turn-key system, which, while expensive, is stable, and the complexity does not interfere with the experience of the user. Though in general, statements on ease of use and stability might be considered anecdotal and may not belong in a scientific article, unreferenced or without data.

(2) One of the major limitations of the first generation LLSM was the use of a 5 mm coverslip, which was a hinderance for many users. However, the Zeiss system elegantly solves this problem, and so does Oblique Plane Microscopy (OPM), while the Altair-LSFM retains this feature, which may dissuade widespread adoption. This limitation and how it may be overcome in future iterations is not discussed.

(3) Further, on the point of sample flexibility, all generations of the LLSM, and by the nature of its design, the OPM, can accommodate live-cell imaging with temperature, gas, and humidity control. It is unclear how this would be implemented with the current sample chamber. This limitation would severely limit use cases for cell biologists, for which this microscope is designed. There is no discussion on this limitation or how it may be overcome in future iterations.

(4) The authors' comparison to LLSM is constrained to the "square" lattice, which, as they point out, is the most used optical lattice (though this also might be considered anecdotal). The LLSM original design, however, goes far beyond the square lattice, including hexagonal lattices, the ability to do structured illumination, and greater flexibility in general in terms of light-sheet tuning for different experimental needs, as well as not being limited to just sample scanning. Thus, the Alstair-LSFM cannot compare to the original LLSM in terms of versatility, even if comparisons to the resolution provided by the square lattice are fair.

(5) There is no demonstration of the system's live-imaging capabilities or temporal resolution, which is the main advantage of existing light-sheet systems.

While the microscope is well designed and completely open source, it will require experience with optics, electronics, and microscopy to implement and align properly. Experience with custom machining or soliciting a machine shop is also necessary. Thus, in my opinion, it is unlikely to be implemented by a lab that has zero prior experience with custom optics or can hire someone who does. Altair-LSFM may not be as easily adaptable or implementable as the authors describe or perceive in any lab that is interested, even if they can afford it. The authors indicate they will offer "workshops," but this does not necessarily remove the barrier to entry or lower it, perhaps as significantly as the authors describe.

There is a claim that this design is easily adaptable. However, the requirement of custom-machined baseplates and in silico optimization of the optical path basically means that each new instrument is a new design, even if the Navigate software can be used. It is unclear how Altair-LSFM demonstrates a modular design that reduces times from conception to optimization compared to previous implementations.

Reviewer #3 (Public review):

Summary:

This manuscript introduces a high-resolution, open-source light-sheet fluorescence microscope optimized for sub-cellular imaging.

The system is designed for ease of assembly and use, incorporating a custom-machined baseplate and in silico optimized optical paths to ensure robust alignment and performance. The authors demonstrate lateral and axial resolutions of ~235 nm and ~350 nm after deconvolution, enabling imaging of sub-diffraction structures in mammalian cells.

The important feature of the microscope is the clever and elegant adaptation of simple gaussian beams, smart beam shaping, galvo pivoting and high NA objectives to ensure a uniform thin light-sheet of around 400 nm in thickness, over a 266 micron wide Field of view, pushing the axial resolution of the system beyond the regular diffraction limited-based tradeoffs of light-sheet fluorescence microscopy.

Compelling validation using fluorescent beads and multicolor cellular imaging highlights the system's performance and accessibility. Moreover, a very extensive and comprehensive manual of operation is provided in the form of supplementary materials. This provides a DIY blueprint for researchers who want to implement such a system.

Strengths:

(1) Strong and accessible technical innovation:

With an elegant combination of beam shaping and optical modelling, the authors provide a high-resolution light-sheet system that overcomes the classical light-sheet tradeoff limit of a thin light-sheet and a small field of view. In addition, the integration of in silico modelling with a custom-machined baseplate is very practical and allows for ease of alignment procedures. Combining these features with the solid and super-extensive guide provided in the supplementary information, this provides a protocol for replicating the microscope in any other lab.

(2) Impeccable optical performance and ease of mounting of samples:

The system takes advantage of the same sample-holding method seen already in other implementations, but reduces the optical complexity. At the same time, the authors claim to achieve similar lateral and axial resolution to Lattice-light-sheet microscopy (although without a direct comparison (see below in the "weaknesses" section). The optical characterization of the system is comprehensive and well-detailed. Additionally, the authors validate the system imaging sub-cellular structures in mammalian cells.

(3) Transparency and comprehensiveness of documentation and resources:

A very detailed protocol provides detailed documentation about the setup, the optical modeling, and the total cost.

Weaknesses:

(1) Limited quantitative comparisons:

Although some qualitative comparison with previously published systems (diSPIM, lattice light-sheet) is provided throughout the manuscript, some side-by-side comparison would be of great benefit for the manuscript, even in the form of a theoretical simulation. While having a direct imaging comparison would be ideal, it's understandable that this goes beyond the interest of the paper; however, a table referencing image quality parameters (taken from the literature), such as signal-to-noise ratio, light-sheet thickness, and resolutions, would really enhance the features of the setup presented. Moreover, based also on the necessity for optical simplification, an additional comment on the importance/difference of dual objective/single objective light-sheet systems could really benefit the discussion.

(2) Limitation to a fixed sample:

In the manuscript, there is no mention of incubation temperature, CO₂ regulation, Humidity control, or possible integration of commercial environmental control systems. This is a major limitation for an imaging technique that owes its popularity to fast, volumetric, live-cell imaging of biological samples.

(3) System cost and data storage cost:

While the system presented has the advantage of being open-source, it remains relatively expensive (considering the 150k without laser source and optical table, for example). The manuscript could benefit from a more direct comparison of the performance/cost ratio of existing systems, considering academic settings with budgets that most of the time would not allow for expensive architectures. Moreover, it would also be beneficial to discuss the adaptability of the system, in case a 30k objective could not be feasible. Will this system work with different optics (with the obvious limitations coming with the lower NA objective)? This could be an interesting point of discussion. Adaptability of the system in case of lower budgets or more cost-effective choices, depending on the needs.

Last, not much is said about the need for data storage. Light-sheet microscopy's bottleneck is the creation of increasingly large datasets, and it could be beneficial to discuss more about the storage needs and the quantity of data generated.

Conclusion:

Altair-LSFM represents a well-engineered and accessible light-sheet system that addresses a longstanding need for high-resolution, reproducible, and affordable sub-cellular light-sheet imaging. While some aspects-comparative benchmarking and validation, limitation for fixed samples-would benefit from further development, the manuscript makes a compelling case for Altair-LSFM as a valuable contribution to the open microscopy scientific community.

Author response:

eLife Assessment

This useful study presents Altair-LSFM, a solid and well-documented implementation of a light-sheet fluorescence microscope (LSFM) designed for accessibility and cost reduction. While the approach offers strengths such as the use of custom-machined baseplates and detailed assembly instructions, its overall impact is limited by the lack of live-cell imaging capabilities and the absence of a clear, quantitative comparison to existing LSFM platforms. As such, although technically competent, the broader utility and uptake of this system by the community may be limited.

We thank the reviewers and editors for their thoughtful evaluation of our work and for recognizing the technical strengths of the Altair-LSFM platform, including the custom-machined baseplates and detailed documentation provided to support accessibility and reproducibility. We respectfully disagree, however, with the assessment that the system lacks live-cell imaging capabilities. We are fully confident in the system’s suitability for live-cell applications and will demonstrate this by including representative live-cell imaging data in the revised manuscript, along with detailed instructions for implementing environment control. Moreover, we will expand our discussion to include a broader, more quantitative comparison to existing LSFM platforms—highlighting trade-offs in cost, performance, and accessibility—to better contextualize Altair’s utility and adaptability across diverse research settings.

Public Reviews:

Reviewer #1 (Public review):

Summary:

The article presents the details of the high-resolution light-sheet microscopy system developed by the group. In addition to presenting the technical details of the system, its resolution has been characterized and its functionality demonstrated by visualizing subcellular structures in a biological sample.

Strengths:

(1) The article includes extensive supplementary material that complements the information in the main article.

(2) However, in some sections, the information provided is somewhat superficial.

Our goal was to make the supplemental content as comprehensive and useful as possible. In addition to the materials provided with the manuscript, our intention is for the online documentation (available at thedeanlab.github.io/altair) to serve as a living resource that evolves in response to user feedback. For this reason, we are especially interested in identifying and expanding any sections that are perceived as superficial, and we would greatly appreciate the reviewer’s guidance on which areas would benefit from further elaboration.

Weaknesses:

(1) Although a comparison is made with other light-sheet microscopy systems, the presented system does not represent a significant advance over existing systems. It uses high numerical aperture objectives and Gaussian beams, achieving resolution close to theoretical after deconvolution. The main advantage of the presented system is its ease of construction, thanks to the design of a perforated base plate.

We appreciate the reviewer’s assessment and the opportunity to clarify our intent. Our primary goal was not to introduce new optical functionality beyond that of existing high-performance light-sheet systems, but rather to reduce the barrier to entry for non-specialist labs.

(2) Using similar objectives (Nikon 25x and Thorlabs 20x), the results obtained are similar to those of the LLSM system (using a Gaussian beam without laser modulation). However, the article does not mention the difficulties of mounting the sample in the implemented configuration.

We agree that there are practical challenges associated with handling 5 mm diameter coverslips. However, the Nikon 25x can readily be replaced by a Zeiss W Plan-Apochromat 20x/1.0 objective, which eliminates the need for the 5 mm coverslip[1]. In the revised manuscript, we will more explicitly detail the practical challenges in handling a 5 mm coverslip and mention the alternative detection objective.

(3) The authors present a low-cost, open-source system. Although they provide open source code for the software (navigate), the use of proprietary electronics (ASI, NI, etc.) makes the system relatively expensive. Its low cost is not justified.

We understand the reviewer’s concern regarding the use of proprietary control hardware such as the ASI Tiger Controller and NI data acquisition cards. While lower-cost alternatives for analog and digital control (e.g., microcontroller-based systems) do exist, our choice was intentional. By relying on a unified and professionally supported platform, we minimize the complexity of sourcing, configuring, and integrating components from disparate vendors—each of which would otherwise demand specialized technical expertise. Moreover, in future releases, we aim to further streamline the system by eliminating the need for the NI card, consolidating all optoelectronic control through the ASI Tiger Controller. This approach allows users to purchase a fully assembled and pre-configured system that can be operational with minimal effort.

It is worth noting that the ASI components are not the primary cost driver. The full set—including XYZ and focusing stages, a filter wheel, a tube lens, the Tiger Controller, and basic optomechanical adapters—costs approximately $27,000, or ~18% of the total system cost. Additional cost reductions are possible. For example, replacing the motorized sample positioning and focusing stages with manual alternatives could reduce the cost by ~$12,000. However, this would eliminate key functionality such as autofocusing, 3D tiling, and multi-position acquisition. Open-source mechanical platforms such as OpenFlexure could in principle be adapted, but they would require custom assembly and would need to be integrated into our control software. Similarly, the filter wheel could be omitted in favor of a multi-band emission filter, reducing the cost by ~$5,000. However, this comes at the expense of increased spectral crosstalk, often necessitating spectral unmixing. An industrial CMOS camera—such as the Ximea MU196CR-ON, recently demonstrated in a Direct View Oblique Plane Microscopy configuration[2]—could substitute for the sCMOS cameras typically used in high-end imaging. However, these industrial sensors often exhibit higher noise floors and lower dynamic range, limiting sensitivity for low-signal imaging applications.

While a $150,000 system represents a significant investment, we consider it relatively cost-effective in the context of advanced light-sheet microscopy. For comparison, commercially available systems with similar optical performance—such as LLSM systems from 3i or Zeiss—are several-fold more expensive.

(4) The fibroblast images provided are of exceptional quality. However, these are fixed samples. The system lacks the necessary elements for monitoring cells in vivo, such as temperature or pH control.

We thank the reviewer for their positive comment regarding the quality of our fibroblast images. As noted, the current manuscript focuses on the optical design and performance characterization of the system, using fixed specimens to validate resolution and imaging stability. We acknowledge the importance of environmental control for live-cell imaging. Temperature regulation is routinely implemented in our lab using flexible adhesive heating elements paired with a power supply and PID controller. For pH stabilization in systems that lack a 5% CO2 atmosphere, we typically supplement the imaging medium with 10–25 mM HEPES buffer. In the revised manuscript, we will introduce a modified sample chamber capable of maintaining user-specified temperatures, along with detailed assembly instructions. We will also include representative live-cell imaging data to demonstrate the feasibility of in vitro imaging using this system.

Reviewer #2 (Public review):

Summary:

The authors present Altair-LSFM (Light Sheet Fluorescence Microscope), a high-resolution, open-source microscope, that is relatively easy to align and construct and achieves sub-cellular resolution. The authors developed this microscope to fill a perceived need that current open-source systems are primarily designed for large specimens and lack sub-cellular resolution or are difficult to construct and align, and are not stable. While commercial alternatives exist that offer sub-cellular resolution, they are expensive. The authors' manuscript centers around comparisons to the highly successful lattice light-sheet microscope, including the choice of detection and excitation objectives. The authors thus claim that there remains a critical need for high-resolution, economical, and easy-to-implement LSFM systems.

Strengths:

The authors succeed in their goals of implementing a relatively low-cost (~ USD 150K) open-source microscope that is easy to align. The ease of alignment rests on using custom-designed baseplates with dowel pins for precise positioning of optics based on computer analysis of opto-mechanical tolerances, as well as the optical path design. They simplify the excitation optics over Lattice light-sheet microscopes by using a Gaussian beam for illumination while maintaining lateral and axial resolutions of 235 and 350 nm across a 260-um field of view after deconvolution. In doing so they rest on foundational principles of optical microscopy that what matters for lateral resolution is the numerical aperture of the detection objective and proper sampling of the image field on to the detection, and the axial resolution depends on the thickness of the light-sheet when it is thinner than the depth of field of the detection objective. This concept has unfortunately not been completely clear to users of high-resolution light-sheet microscopes and is thus a valuable demonstration. The microscope is controlled by an open-source software, Navigate, developed by the authors, and it is thus foreseeable that different versions of this system could be implemented depending on experimental needs while maintaining easy alignment and low cost. They demonstrate system performance successfully by characterizing their sheet, point-spread function, and visualization of sub-cellular structures in mammalian cells, including microtubules, actin filaments, nuclei, and the Golgi apparatus.

We thank the reviewer for their thoughtful summary of our work. We are pleased that the foundational optical principles, design rationale, and emphasis on accessibility came through clearly. We agree that the approach used to construct the microscope is highly modular, and we anticipate that these design principles will serve as the basis for additional system variants tailored to specific biological samples and experimental contexts. To support this, we provide all Zemax simulations and CAD files openly on our GitHub repository, enabling advanced users to build upon our design and create new functional variants of the Altair system.

Weaknesses:

There is a fixation on comparison to the first-generation lattice light-sheet microscope, which has evolved significantly since then:

(1) The authors claim that commercial lattice light-sheet microscopes (LLSM) are "complex, expensive, and alignment intensive", I believe this sentence applies to the open-source version of LLSM, which was made available for wide dissemination. Since then, a commercial solution has been provided by 3i, which is now being used in multiple cores and labs but does require routine alignments. However, Zeiss has also released a commercial turn-key system, which, while expensive, is stable, and the complexity does not interfere with the experience of the user. Though in general, statements on ease of use and stability might be considered anecdotal and may not belong in a scientific article, unreferenced or without data.

The referee is correct that our comparisons reference the original LLSM design, which was simultaneously disseminated as an open-source platform and commercialized by 3i. While we acknowledge that newer variants of LLSM have been developed—including systems incorporating adaptive optics[3] and the MOSAIC platform (which remains unpublished)—the original implementation remains the most widely described and cited in the literature. It is therefore the most appropriate point of comparison for contextualizing Altair’s performance, complexity, and accessibility. Importantly, this version of LLSM is far from obsolete; it continues to be one of the most commonly used imaging systems at Janelia Research Campus’s Advanced Imaging Center.

We acknowledge that more recent commercial implementation by Zeiss has addressed several of the practical limitations associated with the original design. In particular, we agree that the Zeiss Lattice Lightsheet 7 system, which integrates a meniscus lens to facilitate oblique imaging through a coverslip, offers a user-friendly experience—albeit with a modest tradeoff in resolution (reported deskewed resolution: 330 nm × 330 nm × 500–1000 nm).

While we recognize that statements on usability and stability can be subjective, one objective proxy for system complexity is the number of optical elements that require precise alignment during assembly. The original LLSM setup includes approximately 29 optical components that must each be carefully positioned laterally, angularly, and coaxially along the optical path. In contrast, the first-generation Altair system contains only 9 such elements. By this metric, Altair is considerably simpler to assemble and align, supporting our overarching goal of making high-resolution light-sheet imaging more accessible to non-specialist laboratories. In the revised manuscript, we will clarify the scope of our comparison and provide more precise language about what we mean by complexity (e.g., number of optical elements needed to align).

(2) One of the major limitations of the first generation LLSM was the use of a 5 mm coverslip, which was a hinderance for many users. However, the Zeiss system elegantly solves this problem, and so does Oblique Plane Microscopy (OPM), while the Altair-LSFM retains this feature, which may dissuade widespread adoption. This limitation and how it may be overcome in future iterations is not discussed.

We agree that the use of 5 mm diameter coverslips, while enabling high-NA imaging in the current Altair-LSFM configuration, may serve as an inconvenience for many users. We will discuss this more explicitly in the revised manuscript. Specifically, we note that changing the detection objective is sufficient to eliminate the need for a 5 mm coverslip. For example, as demonstrated in Moore et al., Lab Chip 2021, pairing the Zeiss W Plan-Apochromat 20x/1.0 objective with the Thorlabs TL20X-MPL allows imaging beyond the physical surfaces of both objectives, removing the constraint imposed by small-format coverslips[1]. In the revised manuscript, we will propose this modification as a straightforward path for increasing compatibility with more conventional sample mounting formats.

(3) Further, on the point of sample flexibility, all generations of the LLSM, and by the nature of its design, the OPM, can accommodate live-cell imaging with temperature, gas, and humidity control. It is unclear how this would be implemented with the current sample chamber. This limitation would severely limit use cases for cell biologists, for which this microscope is designed. There is no discussion on this limitation or how it may be overcome in future iterations.

We appreciate the reviewer’s emphasis on the importance of environmental control for live-cell imaging applications. It is worth noting that the original LLSM design, including the system commercialized by 3i, provided temperature control only, without integrated gas or humidity regulation. Despite this, it has been successfully used by a wide range of scientists to generate important biological insights.

We agree that both OPM and the Zeiss implementation of LLSM offer clear advantages in terms of environmental control, as we previously discussed in detail in Sapoznik et al., eLife, 2020[4]. However, assembly of high numerical aperture OPM systems is highly technical, and no open-source variant of OPM delivers sub-cellular scale resolution yet.

(4) The authors' comparison to LLSM is constrained to the "square" lattice, which, as they point out, is the most used optical lattice (though this also might be considered anecdotal). The LLSM original design, however, goes far beyond the square lattice, including hexagonal lattices, the ability to do structured illumination, and greater flexibility in general in terms of light-sheet tuning for different experimental needs, as well as not being limited to just sample scanning. Thus, the Alstair-LSFM cannot compare to the original LLSM in terms of versatility, even if comparisons to the resolution provided by the square lattice are fair.

We thank the reviewer for this comment. It is true that our discussion focused primarily on the square lattice implementation of LLSM. While this could be viewed as a subset of the system’s broader capabilities, we chose this focus intentionally, as the square lattice remains by far the most commonly used variant in practice. Even in the original LLSM publication, 16 out of 20 figure subpanels utilized the square lattice, with only one panel each representing the hexagonal lattice in SIM mode, a standard Bessel beam in incoherent SIM mode, a hex lattice in dithered mode, and a single Bessel in dithered mode. This usage pattern largely reflects the operational simplicity of the square lattice: it minimizes sidelobe growth and enables more straightforward alignment and data processing compared to hexagonal or structured illumination modes.

In 2019, we performed an exhaustive accounting of published illumination modes in LLSM and found that the SIM mode had only been used in two additional peer-reviewed publications at that time. We will consider updating this table in the revised manuscript and will expand our discussion to acknowledge the broader flexibility of the LLSM platform—including its capacity for structured illumination and alternative light-sheet geometries. However, we will also emphasize that, despite these advanced capabilities, the square lattice remains the dominant mode used by the community and therefore serves as a fair and practical benchmark for comparison.

(5) There is no demonstration of the system's live-imaging capabilities or temporal resolution, which is the main advantage of existing light-sheet systems.

In the revised manuscript, we will include a demonstration of live-cell imaging to directly validate the system’s suitability for dynamic biological applications. We will also characterize the temporal resolution of the system. As a sample-scanning microscope, the imaging speed is primarily limited by the performance of the Z-piezo stage. For simplicity and reduced optoelectronic complexity, we currently power the piezo through the ASI Tiger Controller. We will expand the supplementary material to describe the design criteria behind this choice, including potential trade-offs, and provide data quantifying the achievable volume rates under typical operating conditions.

While the microscope is well designed and completely open source, it will require experience with optics, electronics, and microscopy to implement and align properly. Experience with custom machining or soliciting a machine shop is also necessary. Thus, in my opinion, it is unlikely to be implemented by a lab that has zero prior experience with custom optics or can hire someone who does. Altair-LSFM may not be as easily adaptable or implementable as the authors describe or perceive in any lab that is interested, even if they can afford it. The authors indicate they will offer "workshops," but this does not necessarily remove the barrier to entry or lower it, perhaps as significantly as the authors describe.

We appreciate the reviewer’s perspective and agree that building any high-performance custom microscope—Altair-LSFM included—requires a baseline familiarity with optics and instrumentation. Our goal is not to eliminate this requirement entirely, but to significantly reduce the technical and logistical barriers that typically accompany custom light-sheet microscope construction.

Importantly, no machining experience or in-house fabrication capabilities are required—users can simply submit provided design files and specifications directly to the vendor. We will make this process as straightforward as possible by supplying detailed instructions, recommended materials, and vendor-ready files. Additionally, we draw encouragement from the success of related efforts such as mesoSPIM, which has seen over 30 successful implementations worldwide using a similar model of exhaustive online documentation, open-source control software, and community support through user meetings and workshops.

We recognize that documentation alone is not always sufficient, and we are committed to further lowering barriers to adoption. To this end, we are actively working with commercial vendors to streamline procurement and reduce the logistical burden on end users. Additionally, Altair-LSFM is supported by a Biomedical Technology Development and Dissemination (BTDD) grant, which provides dedicated resources for hosting workshops, offering real-time community support, and generating supplementary materials such as narrated video tutorials. We will expand our discussion in the revised manuscript to better acknowledge these implementation challenges and outline our ongoing strategies for supporting a broad and diverse user base.

There is a claim that this design is easily adaptable. However, the requirement of custom-machined baseplates and in silico optimization of the optical path basically means that each new instrument is a new design, even if the Navigate software can be used. It is unclear how Altair-LSFM demonstrates a modular design that reduces times from conception to optimization compared to previous implementations.

We appreciate the reviewer’s comment and agree that our language regarding adaptability may have been too strong. It was not our intention to suggest that the system can be easily modified without prior experience. Meaningful adaptations of the optical or mechanical design would require users to have expertise in optical layout, optomechanical design, and alignment.

That said, for labs with sufficient expertise, we aim to facilitate such modifications by providing comprehensive resources—including detailed Zemax simulations, CAD models, and alignment documentation. These materials are intended to reduce the development burden for those seeking to customize the platform for specific experimental needs.

In the revised manuscript, we will clarify this point and explicitly state in the discussion what technical expertise is required to modify the system. We will also revise our language around adaptability to better reflect the intended audience and realistic scope of customization.

Reviewer #3 (Public review):

Summary:

This manuscript introduces a high-resolution, open-source light-sheet fluorescence microscope optimized for sub-cellular imaging.

The system is designed for ease of assembly and use, incorporating a custom-machined baseplate and in silico optimized optical paths to ensure robust alignment and performance. The authors demonstrate lateral and axial resolutions of ~235 nm and ~350 nm after deconvolution, enabling imaging of sub-diffraction structures in mammalian cells.

The important feature of the microscope is the clever and elegant adaptation of simple gaussian beams, smart beam shaping, galvo pivoting and high NA objectives to ensure a uniform thin light-sheet of around 400 nm in thickness, over a 266 micron wide Field of view, pushing the axial resolution of the system beyond the regular diffraction limited-based tradeoffs of light-sheet fluorescence microscopy.

Compelling validation using fluorescent beads and multicolor cellular imaging highlights the system's performance and accessibility. Moreover, a very extensive and comprehensive manual of operation is provided in the form of supplementary materials. This provides a DIY blueprint for researchers who want to implement such a system.

Strengths:

(1) Strong and accessible technical innovation: With an elegant combination of beam shaping and optical modelling, the authors provide a high-resolution light-sheet system that overcomes the classical light-sheet tradeoff limit of a thin light-sheet and a small field of view. In addition, the integration of in silico modelling with a custom-machined baseplate is very practical and allows for ease of alignment procedures. Combining these features with the solid and super-extensive guide provided in the supplementary information, this provides a protocol for replicating the microscope in any other lab.

(2) Impeccable optical performance and ease of mounting of samples: The system takes advantage of the same sample-holding method seen already in other implementations, but reduces the optical complexity. At the same time, the authors claim to achieve similar lateral and axial resolution to Lattice-light-sheet microscopy (although without a direct comparison (see below in the "weaknesses" section). The optical characterization of the system is comprehensive and well-detailed. Additionally, the authors validate the system imaging sub-cellular structures in mammalian cells.

(3) Transparency and comprehensiveness of documentation and resources: A very detailed protocol provides detailed documentation about the setup, the optical modeling, and the total cost.

Weaknesses:

(1) Limited quantitative comparisons: Although some qualitative comparison with previously published systems (diSPIM, lattice light-sheet) is provided throughout the manuscript, some side-by-side comparison would be of great benefit for the manuscript, even in the form of a theoretical simulation. While having a direct imaging comparison would be ideal, it's understandable that this goes beyond the interest of the paper; however, a table referencing image quality parameters (taken from the literature), such as signal-to-noise ratio, light-sheet thickness, and resolutions, would really enhance the features of the setup presented. Moreover, based also on the necessity for optical simplification, an additional comment on the importance/difference of dual objective/single objective light-sheet systems could really benefit the discussion.

In the revised manuscript, we will expand our discussion to include a broader range of light-sheet microscope designs and imaging modes, including both single- and dual-objective configurations. We agree that highlighting the trade-offs between these approaches—such as working distance, sample geometry constraints, and alignment complexity—will enhance the overall context and utility of the manuscript.

To further aid comparison, we will include a summary table referencing key image quality parameters such as lateral and axial resolution, and illumination beam NA for Altair-LSFM. Where available, we will reference values from published work—such as the axial resolution reported in Valm et al. (Nature, 2017)—to provide a clearer benchmark. Because such comparisons can be technically nuanced, especially when comparing across systems with different geometries and sample mounting constraints, we will also include a supplementary note outlining the assumptions and limitations of these comparisons.

(2) Limitation to a fixed sample: In the manuscript, there is no mention of incubation temperature, CO₂ regulation, Humidity control, or possible integration of commercial environmental control systems. This is a major limitation for an imaging technique that owes its popularity to fast, volumetric, live-cell imaging of biological samples.

We thank the reviewer for highlighting this important consideration. In the revised manuscript, we will provide a detailed description of how temperature control can be implemented using flexible adhesive heating elements, a power supply, and a PID controller. Step-by-step assembly instructions and recommended components will be included to facilitate adoption by users interested in live-cell imaging. We also note that most light-sheet microscopy systems capable of sub-cellular resolution—including the original LLSM design, diSPIM, and ASLM—typically do not incorporate integrated CO2 or humidity control. These systems often rely on HEPES-buffered media to maintain pH stability, which is generally sufficient for short- to intermediate-term imaging. While full environmental control may be necessary for extended time-lapse studies, it is not a prerequisite for high-resolution volumetric imaging in many applications. Nonetheless, we will include a discussion of the challenges associated with adding CO2 and humidity control to open or semi-enclosed architectures like Altair-LSFM, and outline potential future paths for integration with commercial incubation systems.

(3) System cost and data storage cost: While the system presented has the advantage of being open-source, it remains relatively expensive (considering the 150k without laser source and optical table, for example). The manuscript could benefit from a more direct comparison of the performance/cost ratio of existing systems, considering academic settings with budgets that most of the time would not allow for expensive architectures. Moreover, it would also be beneficial to discuss the adaptability of the system, in case a 30k objective could not be feasible. Will this system work with different optics (with the obvious limitations coming with the lower NA objective)? This could be an interesting point of discussion. Adaptability of the system in case of lower budgets or more cost-effective choices, depending on the needs.

We thank the reviewer for raising this important point. First, we would like to clarify that the quoted $150k cost estimate includes the optical table and laser source. We apologize for any confusion and will communicate this more effectively in the revised manuscript.

We agree that adaptability is a key concern, especially in academic settings with limited budgets. The detection path can be readily altered depending on experimental needs and cost constraints. For example, in our discussion of alternatives to the 5 mm coverslip geometry, we will describe how switching to a Zeiss W Plan-Apochromat 20x/1.0 in combination with a compatible excitation objective allows high-resolution imaging while accommodating more conventional sample formats. We will expand this to include cost-effective alternatives as well.

We will also expand our discussion on cost-reduction strategies and the associated trade-offs. These include replacing motorized stages with manual ones, omitting the filter wheel in favor of a multi-band emission filter, or using industrial-grade cameras in place of scientific CMOS detectors. While each change entails some loss in functionality or sensitivity, such modifications allow users to tailor the system to their specific budget and application.

Finally, we recognize the challenge in communicating exact costs of commercial systems due to variability in configuration and pricing. Nonetheless, we will include approximate figures where possible and note that comparable commercial systems—such as LLSM platforms from 3i and Zeiss—are several-fold more expensive than the system presented here.

Last, not much is said about the need for data storage. Light-sheet microscopy's bottleneck is the creation of increasingly large datasets, and it could be beneficial to discuss more about the storage needs and the quantity of data generated.

Data storage is indeed a critical consideration in light-sheet microscopy. In the revised manuscript, we will provide a note outlining typical volume dimensions for live-cell imaging experiments along with the associated data overhead. This will include estimates for voxel counts, bit depth, time-lapse acquisitions, and multi-channel datasets to help users anticipate storage needs. We will also briefly discuss strategies for managing large datasets, file types and compression formats.

Conclusion:

Altair-LSFM represents a well-engineered and accessible light-sheet system that addresses a longstanding need for high-resolution, reproducible, and affordable sub-cellular light-sheet imaging. While some aspects-comparative benchmarking and validation, limitation for fixed samples-would benefit from further development, the manuscript makes a compelling case for Altair-LSFM as a valuable contribution to the open microscopy scientific community.

References

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(3) Liu, T. L. et al. Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Science 360 (2018). https://doi.org/10.1126/science.aaq1392

(4) Sapoznik, E. et al. A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics. eLife 9 (2020). https://doi.org/10.7554/eLife.57681

(5) Huisken, J. & Stainier, D. Y. Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM). Opt Lett 32, 2608-2610 (2007). https://doi.org/10.1364/ol.32.002608

(6) Ricci, P. et al. Removing striping artifacts in light-sheet fluorescence microscopy: a review. Prog Biophys Mol Biol 168, 52-65 (2022). https://doi.org/10.1016/j.pbiomolbio.2021.07.003

  1. Howard Hughes Medical Institute
  2. Wellcome Trust
  3. Max-Planck-Gesellschaft
  4. Knut and Alice Wallenberg Foundation