Run the microscope from one app. Then find the answer in the pictures.

Cameras: Thorlabs uc480 (DCx) and Andor SDK2 cameras through their vendor drivers on Windows, USB cameras, the computer's own camera, and phones with the SciCope app. Stages: Marlin boards (Creality-style controllers, the Ender S1 Plus build) and GRBL boards (Arduino with a CNC shield) on a serial port — X and Z plus a rotating plate. Light: NI-DAQmx digital outputs (relays) on Windows. Focus: Optotune lens drivers. The Devices dialog lists the ports and cameras it can see.

Yes. Any single camera works on its own — pictures, timelapses, the analysis tools and the assistant. The demo microscope simulates a camera, a stage, a light and a lens together, so every feature can be tried with nothing plugged in.

Only after you allow it. Its steps appear as a card; the ones that move the stage, change the focus or start a series wait for Allow, while taking a picture, reading values or opening a view run at once. If you prefer hands-off operation, switch on Let the assistant run the microscope without asking in Settings. The red STOP button and the Escape key stop every move and job at any time.

It tells you. After tracking, the Check panel lists every moment that needs a human: two objects touching, a missing stretch, an impossible jump, and the one that used to ruin a dataset silently — a blob far bigger than one animal. The app compares each detection with the typical size of a single animal in your own pictures and says “one blob looks like 2 animals on frames 10–12”, or “worm 7 walks out of worm 3 at frame 12 — there were 2 animals in that spot from frame 5”. Separate then cuts the blob into worm-sized parts and gives each part back to the right animal, seeded by where each one was heading, so the names do not swap. You can also point at where an animal really is, swap two names, split or merge tracks, and re-track one animal from that frame on. Every correction becomes a fixed point that the automatic passes keep. Two animals lying exactly on top of each other cannot be told apart by any shape-based method — the app shows them sharing a point rather than inventing an answer.

Yes. The Analyze workspace opens any folder of pictures — JPG, PNG or TIFF, including 16-bit — numbered in a sequence, with an optional filter so you can pick every second frame or one channel of an interleaved series. Tell it the scale (µm per pixel) and the time between frames, or calibrate by clicking two points on something of a known length, and every measurement comes out in micrometres and seconds. A detections CSV from an earlier run can be imported back.

No. Detection, tracking, measurement and every export run on the Python inside the app and on the lab's own analysis library — the same code that has been used on the bench for years, rebuilt as a workspace. Fiji is an optional download from Settings › Advanced for tools written as ImageJ macros and for opening microscope file formats such as CZI or ND2 through Bio-Formats.

No. You describe what you want in plain words, and the tool you get is a form with settings in plain words too. If you are curious, Developer mode shows the exact script that runs, and you can keep and reuse every tool. Python and its scientific libraries come with the app; nothing else is installed on the computer.

Your own. In Settings you connect Claude, ChatGPT, Gemini or DeepSeek with an API key, or the Claude Code, Codex or Gemini CLI apps with the subscription you already have. SciCope has no account or subscription of its own; the AI provider bills you directly according to its own terms.

Pictures go into the session folder shown in the Microscope view, numbered with a prefix and, for synchronized captures, the camera's name. Results go into a SciCope results folder inside the session folder, one subfolder per tool and date: a summary table (CSV) with one row per photo, the output pictures and per-photo detail tables. If the folder is in your Google Drive, everything syncs.

Yes. Pictures taken by the desktop app are saved on the computer. Point the Photos view at any folder with Change in the sidebar — including files exported by other microscope software. On the same Wi-Fi the desktop app can also copy a phone's current folder straight to the computer.

Phone apps: Android 8.0 and later, and iPhone with iOS 17 and later. Desktop app: Macs (Apple Silicon and Intel) and 64-bit Windows PCs. The Thorlabs and Andor cameras and the NI relay need their Windows drivers; stages, lenses, USB cameras and phones work on both systems.

The builds are not signed with an Apple Developer ID or a Windows code-signing certificate yet, so macOS shows the “cannot verify the developer” dialog and Windows shows SmartScreen. Both can be passed once as described under First launch. Signed, self-updating builds are planned.

On the desktop, the Analyze workspace and the Make a movie tool build an MP4 from a session folder, using the real frame times from captures.csv; the Microscope view can also record the live picture directly. The phone app can do the same from its Library.

Only what is needed to control a phone from another network: the commands, the camera settings and the live preview, and only after the phone's owner has accepted the computer. Photos and results never pass through it. Lab cameras, stages, lights and lenses are never on the network at all.