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FAQ & Resources

Explore common questions and watch our tutorial video

Frequently Asked Questions

What is the added value of EasyPanel? How does EasyPanel help flow cytometrists?

EasyPanel provides a very strong added value to 100+ leading flow cytometry core facilities and their users by:

-Drastically saving time in the panel design process, not only for large complex conventional/spectral panels but also simplistic panels designed by novice users with introductory experience. 

-QC’ing existing self-designed panels by providing quantified scores on panel quality and comparing them to the algorithm’s top suggestions. EasyPanel identifies the most problematic fluorochrome(s) in suboptimal panels, which contributes the most to your panel spillover/complexity. By removing such fluorochrome(s) and redesigning panels, EasyPanel automatically suggests a panel that may be significantly better.

How can I access my institution's (lab/company/university) EasyPanel account?

To access EasyPanel (featuring your flow core cytometer configurations), visit our website homepage (flow-cytometry.net) and click “Register” or “Login”. If your institution has an EasyPanel license, you and anyone at your institution can sign up directly using their own institution email address and a password of their choice.

What if I have an existing panel that is already designed?

Not only can EasyPanel suggest panels from scratch (suggesting all the fluorochromes in your panel), but our algorithm also supports:

-Partial panel design, letting you build on your existing panel backbone or your existing antibody products inventory

-QC’ing your existing self-designed panels by providing scoring/quantified scores on panel their quality and comparing them to the algorithm’s top suggestions. In case your panel is suboptimal, EasyPanel will identify the most problematic fluorochrome(s) in suboptimal panels, which contributes the most to your panel spillover/complexity. By removing such fluorochrome(s) and redesigning panels, EasyPanel will automatically redesign a panel that may be significantly better

How does licensing work? How much does EasyPanel cost?

We typically offer annual (or semi-annual) institution-wide access licenses to EasyPanel, however, we also accommodate single-seat licenses. 

Institution-wide licenses grant access to everyone at your institution (i.e., everyone who has an email with your institution’s email domain). 

To access EasyPanel (featuring your flow core cytometer configurations), visit our website homepage (flow-cytometry.net) and click “Register” or “Login”. Anyone at your institution can sign up directly using their own institution email address and a password of their choice. 

License costs depend on 2 factors:

-The size of your flow core (number and complexity of instruments, and whether they are conventional/spectral)

-The usage rates of your flow core users/lab members during the 2-3 weeks free trial period after the introductory webinar session.

Does EasyPanel offer a free trial period?

Yes! We provide a webinar session with the flow core manager/flow core users to introduce and demo the tool, as well as answer questions. Afterward, we offer EasyPanel for a 2-3 weeks free trial period (without commitment on your end). 

During that period, we monitor usage to gauge interest/utility. 

At the end of the free trial period, we will share the usage report, statistics, and a corresponding quotation that guarantees significant cost savings (given your estimated usage). 

What does EasyPanel’s algorithm account for when designing a panel?

EasyPanel’s proprietary algorithm considers many factors in the panel design process, including:

-Minimizing spillover between the fluorochromes that constitute the panel

-Matching fluorochromes to markers based on markers’ expression level and fluorochromes’ brightness

-Identifying commercial availability at all vendors of fluorochrome-conjugated antibodies (including but not limited to BD, Biolegend, ThermoFisher, Miltenyi, Novus, R&D Systems, Beckman Coulter, Bio-rad…) 

-Suggesting clones that have been validated in OMIPs (Optimized Multicolor Immunophenotyping Panels)

 

EasyPanel holistically accounts for coexpression by selecting a combination of fluorochromes that minimizes spillover/similarity/complexity for the whole panel. This computational approach often eliminates the need to design around the specific coexpression profiles of individual markers. However, users may always go back and select up to 5 markers as coexpressed on the same cell population (up to 3 different cell populations supported). In this case, the algorithm will focus on matching these specific antigens to fluorochromes that have exceptionally low spillover/similarity.

In addition to EasyPanel’s fully automated panel builder, do you also offer a commercial catalog/manual panel builder and spectrum viewer?

Yes! EasyPanel is a one-stop shop that includes all panel design tools and features.

How does EasyPanel compare with other panel design tools?

EasyPanel is the first (and currently only) fully automated panel designer and works for all types of cytometers (conventional and spectral). 

Our startup was established by immunologists and software developers in 2020. Since then, we have been gathering and implementing a huge amount of learning, feedback, suggestions, and updates from hundreds of users at leading flow core facilities (academic, biotech, and large pharma).

EasyPanel is a vendor-agnostic platform, meaning that our algorithm never pushes for the suggestion of one product over another based on commercial interests with vendors. Panel suggestions are based solely on the panel optimization criteria considered by our algorithm (see above).

Can users fine-tune or edit the suggested panels?

While we are confident that EasyPanel’s panels are highly optimized, we encourage users to critically review them and provide feedback. You can do so using the “feedback button” that is conveniently found under each panel suggestion. 

Also, we acknowledge the potential limitations of any computer algorithm, including EasyPanel because it is very hard to account for the intricacies of the different experimental conditions, laser intensities/PMTs, and multiple other factors that may affect panel performance. 

We believe that the best panels (especially complex ones) may ultimately derive from a combination of EasyPanel’s intelligence and a user’s own experience. Users may easily fine-tune or edit EasyPanel’s automated panels through the button called “Manually Edit Panel” found under each panel suggestion.

How large can EasyPanel’s suggested panels be?

There is no limitation on the size of our algorithm’s panels except for the guarantee that they do not fall below a certain level of quality, i.e., panels should not exceed a certain level of spillover or complexity, among other factors. Typically, our spectral panels can reach up to 55 colors while ensuring our extremely high panel quality standards. The max size of conventional cytometer panels is understandably slightly less than the total number of channels available; For example, users may typically design/optimize panels of up to 20 to 23 colors on a conventional cytometer equipped with 25 channels. 

Is users’ panel design data secure on EasyPanel? Does EasyPanel share users’ data with third parties?

EasyPanel does not store user-specific or institution-specific panel information! The only information stored are users’ email accounts and passwords (which are hashed), as well as instrument configurations.

EasyPanel is hosted at Digital Ocean and AWS, two large and reputable US-based cloud service providers.

To protect our users’ data, we follow stringent web security measures including the following:

The website and its related subdomains are only accessible through https protocol.

User passwords are saved as hashes not as plain text.

User email accounts must be verified prior to using the account.

Only strong passwords are approved.

License users’ data is fully confidential and is the sole property of the institution or company licensing EasyPanel. EasyPanel does not access nor share such data in any way, shape, or form.

What is the spillover score? Is my spillover score good or bad?

The total spillover score is a single score that quantifies the theoretical quality of a conventional flow cytometry panel. It is one of multiple different criteria taken into consideration by our algorithm. With all other panel design factors held the same, the lower this score is, the less compensation you may have to perform and the better your panel design is.

 

The spillover score is simply the sum of all spillover scores between the different pairs of fluorochromes in your panel, multiplied by a hundred. You can view the individual spillover scores by clicking on the “Spillover Matrix” button located just below your panel table.

The spillover score is a theoretical quantification of the amount of spillover you would get out of a panel. 

 

The total spillover score is a relative number. To judge whether a panel is generally “good” or not, one should compare the spillover score of their panel to the lowest possible spillover score suggested by EasyPanel for that panel. If your panel’s spillover is higher than 1.5X or 2X the lowest possible spillover score, then it may indicate that your panel has room for improvement/reducing spillover by changing your combination of fluorochromes. 

 

While the total spillover score is a very useful quantitative proxy for comparing the quality of different conventional panels, it is a theoretical score that should be interpreted with caution. The actual spread/spillover depends on factors such as your laser intensities, PMTs, how stable your fluorochromes are, how well your instrument is maintained, etc. 

What is the complexity index? Is my complexity index good or bad?

The complexity index is one of the most important quantitative metrics for overall panel quality in spectral cytometry. This score measures the uniqueness of each dye in a given panel. Higher complexity index scores indicate higher overall spread, which presents a potential challenge in spectrally unmixing the dyes in the panel. EasyPanel generally presents the panels with the lowest complexity index possible.  

To get a sense of whether your panel (including your self-chosen fluorochromes) is generally “good” or not, you may compare your complexity score to the lowest possible score given by EasyPanel: If your panel’s complexity score is higher than 1.5X or 2Xthe EasyPanel fully-designed panel score, this may indicate that your panel has room for improvement by choosing a different combination of fluorochromes. 

What is the similarity index?

The similarity index is a scale from 0 to 1, characterizing how unique the spectral signature of one fluorochrome is compared to another one in spectral cytometry. This index is useful to assess how well each pair of dyes will be unmixed. Values close to 1 indicates that the two compared fluorochromes have very similar signatures and will be hard to unmix. Such pairings should be avoided for markers that are coexpressed on the same cell population.

What species reactivity does EasyPanel support?

EasyPanel supports products with all species reactivities commercially available including Human, Mouse, Rat, Non-Human Primate, Dog, Pig, Chicken…

Can EasyPanel provide guarantees about the panels suggested?

Since our establishment in 2021, we have quickly and carefully implemented a huge amount of learning, feedback, suggestions and updates from hundreds of users at leading flow core facilities (academic, biotech and large pharma). We are confident that panels suggested by EasyPanel are generally very good and highly reliable. 

Many of EasyPanel’s suggestions have been experimentally tested and validated by users. They have been presented at multiple conferences, including Cyto 2023. Several papers citing EasyPanel are currently under review and will hopefully be published soon (2024).

Please note, however, that EasyPanel cannot provide a legal guarantee about the performance of any panels because this ultimately relies on several other factors beyond our control, including clone selection, product handling, antibody titration, sample preparation and staining, instrument performance and settings. 

Can I add fluorescent proteins into EasyPanel?

Yes, absolutely! Simply, just create a marker (that you may call whatever you prefer, e.g., “Gene Expression My Experiment 2023”) and match it to any fluorescent protein via the drop-down list of fluorochromes (e.g., GFP, mCherry, tdTomato, mOrange…)

Does EasyPanel account for cells autofluorescence?

EasyPanel’s algorithm is designed to be able to account for your sample’s autofluorescence signal. Please share the corresponding data (spectral profile of your autofluorescence signal), ideally as an fcs file, and we will get it added for you in the fluorochromes/dyes dropdown list so that you are able to choose it and let the tool account for it.