Microscopy acquisition planner

Build with Vlak
Slide 07Acquisition planning
Local draft
01 / Planning

Stage positions

Draft

3 of 3 positions included. Select a record, then edit its coordinates.

Position records

Coordinate frame: Slide-local frame (slide-local)

Selected: Upper field (site-01)

  1. X (µm)
    -240
    Y (µm)
    180
    Z (µm)
    0

    Included in plan

  2. X (µm)
    0
    Y (µm)
    0
    Z (µm)
    2

    Included in plan

  3. X (µm)
    220
    Y (µm)
    -160
    Z (µm)
    -1

    Included in plan

Coordinate context
Coordinate frame

Assigning a frame or unit label does not convert coordinates. Only use labels that match your supplied values.

X unit
Y unit
Z unit
120 planned framesNot acquired
Example stage · Slide-local frameNo instrument connected

Slide 07 · spatial survey

Draft worksheet · schema vlak.microscopy-plan · version 1

Content fingerprint: fnv1a-e27261ca. Identifies the applied plan values printed below.

Planned frames
120
Total exposure
3.9 s
Units
X µm · Y µm · Z µm
Coordinate frame
Slide-local frame

Plan issues

No plan issues recorded.

Ordered positions

  1. Upper field · Included · X -240 µm · Y 180 µm · Z 0 µm
  2. Center field · Included · X 0 µm · Y 0 µm · Z 2 µm
  3. Lower field · Included · X 220 µm · Y -160 µm · Z -1 µm

Capture steps

  1. Reference · channel Transmitted light · exposure 20 ms · time 0 s · depth 0 µm
  2. Signal · channel Channel A · exposure 45 ms · time 0 s · depth 0 µm

Axes

Z: start -2 µm, interval 1 µm, count 5. T: start 0 s, interval 30 s, count 4.

Acquisition state: Not acquired. This worksheet is a review of supplied planning values, not an acquisition record.

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      Edit positions and capture steps → inspect the planned stack → review and export

      View source
      About this download

      A standalone Vite and React project using Vlak 0.5.0. Extract the ZIP, open its folder, then run npm install and npm run dev. Requires Node 22.12 or newer.

      This is a local planning example. No microscope is connected, no images are acquired and no movement is commanded. Exposure totals are arithmetic sums, not acquisition-time estimates.

      Installation and base examples

      Inside the interface

      Prepare a bounded acquisition plan with named stage positions, capture steps and depth and time axes. Inspect the planned coordinates, review the frame count and total exposure, then export the working plan as JSON. Import validates a candidate before replacing the current draft.

      All records are local planning examples. No microscope is connected, no images are acquired and no movement is commanded. Total exposure is an arithmetic sum, not a wall-clock acquisition estimate. JSON exports retain the actual plan and its coordinate units.

      Watch the 20-second walkthrough

      A short walkthrough of the working microscopy acquisition planner study.

      Components used

      Use this as a starting point

      Build with Vlak

      Install the components, add the stylesheet, and bring your own content. The study’s source shows how the pieces fit together.

      React componentsCSS includedMIT licensed

      Download the Microscopy acquisition planner starter

      Install the package
      npm install @noorddev/vlak-react
      import "@noorddev/vlak-react/css";
      Installation guide View study source

      Start with your coding agent

      A ready-to-use brief with this study, Vlak’s components, and the design guide.

      Component modifications

      • Stage position list keeps selection, inclusion and order tied to stable record IDs. Quantity field edits supplied coordinates and exposures without treating missing values as zero.
      • Acquisition sequencer defines the ordered capture steps. Stack navigator inspects planned depth and time coordinates while keeping every frame marked Not acquired.
      • Review validates the working plan before export. Import stages a bounded JSON candidate; malformed files preserve the current records and unsaved position draft.
      • On mobile, Positions, Sequence, Stack and Review are focused screens. Opening a position replaces the list with its editor; Back preserves the unsaved draft, while Apply and Discard remain explicit. The planned stack and import/export controls stay available without shrinking the desktop workspace.