Cube & Imaging — best filters for a single dye
Pick a dye and the app ranks every filter-pair and dichroic in your inventory by predicted photographic brightness on the Sony A7R IV-A, under each of your light sources and illumination modes.
Click any result row to load its filter assembly into the spectrum graph above.
Palette Planner — multi-dye combinations for beautiful images
Tell the planner what specimen you are photographing and it suggests dye combinations, ranked by how well they reveal the tissues present. Each suggestion includes a custom cube assembly from your filter collection.
Click any palette to load its dyes and recommended cube into the spectrum graph above.
Inverse Planner — which dyes work with my light source?
Pick a light source. The planner shows every dye ranked by yield, and each card recommends the best filter cube for that dye. Hover or click a card to see its spectrum above. The Manual Build row inside each card lets you swap parts; click the Recommended pill on the card to snap back.
Click any dye row to plot it against the chosen cube assembly above.
Fluorophore library
Your dye library. Each entry includes spectra, tissue affinities, and an editable protocol (immersion, rinse, mount) with your own notes and history. Uncheck "Available" for dyes you don't own yet; the planners will exclude them automatically.
Fluorophore library
Filters & dichroics
Every excitation and emission bandpass, every long-pass emission, and every dichroic mirror available to you. Click a chip to plot its transmission curve against the dye selected below; uncheck items you don't physically have.
How to read this graph
- Dichroic mirror
- The yellow dashed line marks its cutoff. Light to the left of the line reaches the specimen; light to the right reaches the camera sensor.
- Excitation filter
- Determines what wavelengths of light are sent to the dichroic mirror. These are the wavelengths of light that will cause the specimen to fluoresce. Excitation filters are almost always bandpass, transmitting a narrow slice of the spectrum chosen to match the dye's excitation peak.
- Emission filter
- Designed to pass only certain wavelengths of light to the camera system's sensor. These can be bandpass filters, which transmit a narrow slice of the spectrum, or long-pass filters, which transmit everything above a cutoff wavelength.
- Reading the dye curves
- Each fluorophore appears as two curves: the left peak is the dye's excitation spectrum — the wavelengths that make it fluoresce — and the right peak is its emission spectrum — the wavelengths it gives off when it does.
Each curve on the graph can be hidden by unchecking its box in the legend above the graph. Hover over any chip below for a quick preview, or click on a chip to have it remain in place on the graph.
Dichroic mirrors
Excitation filters
Emission filters
Pre-made cubes — spectrum preview
Click a cube to overlay its excitation, dichroic, and emission filters on the spectrum above. Click again to clear. Marking which cubes you own happens on the My Inventory tab.
● = you own every part of this cube · ○ = at least one part is not in your inventory
Light sources
Check the illuminators you actually have on your microscope. Everyone's setup differs — only checked sources appear in the planners when "use only available" is on.
Light sources
My inventory
Tell the planner what filter cubes and loose optics you actually own. The Filters & Dichroics tab will mark every component you own as available; everything else stays unchecked. You can still override individual filters there for edge cases.
Cubes I own
Check every cube currently in your turret. Each cube auto-checks its excitation filter, dichroic, and emission filter under Filters & Dichroics. Built-in cubes (Nikon, Leica) are grouped below; cubes from other brands go in the Custom cubes section.
Save your real loadout as a baseline, then freely check or uncheck cubes to explore what-ifs — one click restores your saved set. To back up everything (cubes, custom filters, scenes) across devices, use Export my data on the Help & Glossary tab.
Hover any cube card below to see how its excitation, dichroic, and emission line up with this dye. Click still toggles ownership.
Cubes by brand
Custom cubes
A catch-all for cubes you don't want to file under any brand — home-built rigs, anonymous third-party cubes, one-offs, or anything that doesn't fit a brand name. For everything else, scroll up to the brand strip and use + Add a brand… to open or create a brand block (Nikon, Leica, Olympus, your own name, etc.). The cube will live inside its brand and be easier to find later.
Custom cameras
Add any camera that is not on the built-in list (Sony A7R IV-A color, mono-converted). Custom cameras appear in the Camera dropdown at the top of every tab and participate in scoring like the built-in bodies. For a color body, pick Color (RGB Bayer) and the planner will model standard red/green/blue Bayer response. For a converted body, pick Monochrome / full-spectrum and set the UV and IR cut wavelengths.
Loose filters and dichroics
Individual components purchased outside a cube — for example a 25 mm bandpass you slot into the filter holder. Add them under Filters & Dichroics with the existing add buttons; they appear here so you can see them in one place.
What can I see with what I own?
For each fluorophore, the best yield from any cube you own. Excellent (≥ 60% of theoretical max), Good (≥ 30%), Partial (≥ 10%), or None.
Session log
Record each shoot: specimen, dyes used, immersion and rinse times actually used, filter cube assembly, light source, exposure settings, outcome rating, and notes. Each dye's Protocol panel automatically shows your recent session averages.
Glossary
Plain-language definitions, recipes, and practical notes for terms used throughout the app. Cross-linked — terms referenced within definitions become clickable.
User Manual
A short overview at the top, then collapsible reference sections for each tab. Hover any underlined term for a definition.
Quick start
- Tell the app what you own. Open Fluorophores, Filters & Dichroics, and Light Sources. Uncheck anything you don't physically have. Your inventory saves automatically.
- Pick a planner that matches your question.
- I know my dye → Cube & Imaging. Ranks every cube build in your inventory.
- I know my specimen, want a multi-dye look → Palette Planner. Suggests 2–4 dye combinations and the cube to use.
- I have a cube, what dyes will it photograph? → Inverse Planner.
- Read the spectrum graph. The graph shows your light source, dye excitation/emission, and filter passbands stacked on the same wavelength axis. The yellow dashed line marks the dichroic cutoff.
- Log what you actually shot. Use the Session Log tab to record specimen, dyes, exposure, and outcome. Over time the planners become a personal reality check.
- Back up. Use the Export button below before any major change. The
.jsonfile restores everything on any computer.
About this Fluorescence Microscopy Designer
My name is Bud Perrott (Walter W. Perrott). I am a retired radiologist and photomicrographer who uses a Nikon Eclipse E800 for artistic fluorescence, diatom, and crystal imaging, and I designed this application for my own bench work and for anyone who works the same way.
In a standard epifluorescence microscope, the excitation filter, dichroic mirror, and emission filter live together as a matched set inside a filter cube. I designed this application to allow the physical removal of the excitation and emission filters from their original cubes. The excitation filter can be placed in the illumination light path and the emission filter above the objective in the detection path, while the dichroic remains in the turret. An additional option with trans-illuminated light allows the dichroic mirror to be removed entirely — the excitation filter directly illuminates the specimen from below through the condenser, and the emission filter above the objective collects the fluorescence, with no dichroic involved at all.
The planner supports both epi-illumination and transmitted light as fluorescence excitation sources, even though transmitted-light fluorescence is not part of a typical factory configuration. Each cube can be treated either as an intact, manufacturer-designed unit or as a source of individual components that can be mixed and matched across different light paths. The app lets you evaluate both modes of use: classic cubes used as shipped, and custom combinations built from separate excitation, dichroic, and emission elements in either epi or transmitted configurations.
The camera options likewise reflect practical, non-standard use: both color and monochrome-converted digital cameras are available to evaluate, so you can consider how different sensor types will respond to a given fluorophore and filter combination. The goal is to make it easy to explore questions like “What if I use this emission filter from one cube with an excitation filter from another, under transmitted light?” or “How does a monochrome-converted camera respond if I pair this dye with a modified cube configuration?” without constantly digging through datasheets or physically rebuilding cubes at the bench.
It is intended for anyone who wants to treat fluorescence cubes, filters, light sources, and cameras as creative tools rather than fixed accessories, and to keep track of evolving, non-standard setups over time.
Ready to explore the app?
Backup & restore
The planner saves your cubes, custom filters, fluorophores, and saved scenes in this browser on this device. If you clear your browser data or switch browsers or devices, that information is lost. Use Export my data to download a backup file that contains your personal inventory, custom entries, and scenes. Later, use Import data to restore your planner to the same state on this or another browser.
Inventory & sharing
Your inventory is private to your browser. Nothing you check, customize, or save leaves your machine. The same public URL serves everyone, but each visitor's view is built from their own local browser storage:
- You open the link on your Mac — your saved cubes, custom filters, and scenes load, and the green ownership dots and “from cube” footers appear.
- A colleague or student opens the same link on their device — their storage is empty, so they see a clean planner with no dots, no “from” footers, and no legend text. Identical to first launch.
One link, two experiences — you do not need to keep a separate “clean” copy of the app for distribution.
With nothing checked, nothing breaks. The ownership indicators are gated on having at least one cube, custom cube, or filter checked. With an empty inventory the planners run normally, just without the green dots and legends. Each planner result still shows its recommended assembly and the closest matching Nikon cube.
To demo a clean version yourself, open the URL in a private / incognito window — your real saved data is untouched. To share your exact configuration with another person, use Save scene in the header to export a scene file they can load with Load scene.
Tab-by-tab reference
Click any heading below to expand.
Cube & Imaging
Purpose: for one chosen dye, rank every possible excitation filter → dichroic → emission filter combination in your inventory by predicted photographic brightness on your camera, under your chosen light source.
Controls:
- Dye — pick from your fluorophore library.
- Light source — only checked light sources appear here when "Use only my available items" is on.
- Illumination mode — Epi (light through the objective, dichroic in the turret), Trans + filter in holder (light through the condenser with the excitation filter in front of it, no dichroic), or Trans, no filter (broad transmitted light through the condenser, no excitation filter, no dichroic). The two trans modes bypass the dichroic entirely; the emission filter still sits above the objective and selects the fluorescence wavelengths.
- Results shown — how many cube builds to list.
Reading results: each row shows a YIELD score (relative brightness, higher is better), the cube build, and excitation / emission efficiencies. The Recommended (best build) chip flags the top result. ≈ Nikon UV-1A means the build matches a known commercial cube — those are usually a safer starting point than custom builds.
Pre-made cubes: below the ranked builds, factory cubes (Nikon, Leica) appear as chips with their excitation, dichroic, and emission specs. Click any chip to populate the spectrum graph with that exact build.
Tip: if results look too dim, switch the light source. A 365 LED outperforms a xenon for short-UV dyes; a halogen wins for long-emission dyes.
Palette Planner
Purpose: for multi-color work, suggest dye combinations that reveal the tissues in your specimen, plus the cube build to use.
Controls:
- Specimen — pick the tissue type. Each specimen knows which structures it contains (e.g., woody stem → xylem, phloem, cuticle, lignin).
- Palette size — 2, 3, or 4 dyes.
- Light source and illumination mode — same as Cube & Imaging.
Reading results: each card shows the MATCH score, the dye combination as colored chips, the recommended cube build (excitation, dichroic, emission), and which tissue each dye binds (e.g., "Calcofluor White → cellulose, chitin"). Δemission tells you how separated the colors will look on camera — bigger is better for clean color separation.
Tip: if a palette has Δemission below ~40 nm, expect color bleed in the photograph. Try a different palette or a tighter emission bandpass.
Inverse Planner
Purpose: you've already picked a cube assembly (or own a fixed factory cube) — show every dye that will photograph well with it.
Controls: excitation filter, dichroic, emission filter, light source, illumination mode. Each dropdown shows only items you marked Available.
Reading results: dyes ranked by predicted brightness with this exact cube. Useful for asking "what else can I shoot with my Nikon UV-1A?"
Fluorophores
Purpose: your dye library. Each entry includes excitation/emission peaks and bandwidths, tissue affinities, and an editable Protocol panel with immersion, rinse, and mount notes.
Protocols start from the histology literature — refine them from your bench experience. Click any field to edit; the app keeps a short history showing how your technique has evolved. If you've used a dye in the Session Log, recent session averages appear automatically.
Available checkbox — uncheck dyes you don't physically own to exclude them from the planners.
Adding new fluorophores: use the Add button at the top of the tab. Provide ex/em peaks (nm), bandwidths (FWHM), and tissue affinities. The new dye appears immediately in all planners.
Filters & Dichroics
Purpose: every excitation bandpass, emission bandpass or longpass, and dichroic mirror in your inventory.
Spectrum graph stays pinned at the top of the tab and plots transmission curves for the chips you click. It remains visible while you scroll through the chip lists and pre-made cubes.
Pre-made cubes: at the bottom — factory cubes packaged with their three parts. Clicking a cube fills in the chip selection above so you can compare against custom builds. Click None at the end of any section to clear that selection.
Available checkbox — uncheck filters you don't physically own.
Light Sources
Purpose: the illuminators on your microscope (mercury, xenon, halogen, LEDs of various wavelengths, or DIY rigs).
Check the sources you actually have. With Use only my available items on, only checked sources appear in the planners.
The light source's spectrum is used in the planner math — a 365 nm LED scores very differently from a broadband mercury lamp on the same dye.
Session Log
Purpose: a personal logbook for shoots. Record specimen, dyes used, immersion and rinse times, cube assembly, light source, exposure settings, outcome rating, and free-text notes.
Each fluorophore's Protocol panel automatically pulls recent session averages so your starting times reflect what's actually worked for you.
The Session Log is for your own reference — it does not currently influence planner rankings. Treat it as a bench notebook.
Glossary
Purpose: plain-language definitions, recipes, and practical notes for terms used throughout the app.
Open the Glossary tab to browse the full list. Use the category filter and search box to find a term quickly.
Adding new items — three ways
- In-app forms (easiest). Every tab has an Add button at the top. Fill in the form, click Save. The new item appears immediately and persists in your browser.
- Edit
data.jsdirectly. Opensite/data.jsin any text editor. Copy an existing entry, change the numbers, save, reload. - Ask Computer to rebuild. Start a new conversation, describe what you want added, and Computer regenerates the app. Best for big changes or when you need help finding accurate spectra.
A note on accuracy
Scoring uses published dye spectra approximated as Gaussian curves. Real photographic results depend on specimen preparation, staining time, concentration, mountant, optics, and many other factors the app cannot know. Treat the rankings as educated starting points, not guarantees. Over time, your Session Log builds your personal reality check on what actually works on your bench.
Show welcome message again — useful for demoing the first-visit experience to a colleague.