Orchestra Planner is designed to sit upstream of your experimental data.

A typical workflow looks like this:

1. Orchestra Planner
   You design and plan experiments:
   • experiments and projects
   • plates and imaging sessions
   • timing (coating, seeding, imaging, fixation, staining)
   • structured experimental metadata captured early
2. Metadata Extractor (optional companion tool)
   A separate tool that:
   • reads microscope image files
   • extracts acquisition metadata
   • merges them with experimental metadata from Orchestra Planner
3. BFF (BioFile Finder)
   The merged output (CSV) can be used in BFF to:
   • search across all images
   • filter by experimental conditions, timepoints, plates, antibodies, etc.

Orchestra Planner itself does not touch image files.

It focuses on planning, structure, and metadata — leaving data extraction and indexing to dedicated tools.

If this is your first time opening the app, a good starting point is:

1. Create one experiment.
2. Give it an anchor date so it appears in the calendar.
3. Add at least one imaging session.
4. Open a plate map and explore how metadata is entered.
5. Drag the experiment in the calendar to see how scheduling behaves.

In just a few minutes, you should feel comfortable exploring the app without risk — nothing is irreversible.

1. Click “+ Create new experiment” in the left panel.
2. Fill in the experiment metadata (everything can be edited later):
   • Select a project this experiment belongs to (or leave blank)
   • Add a short description
   • Specify the number of plates
   • Enter the primary resource (e.g. imaging platform)

   For each Imaging Session:

   • Define the imaging duration (in days)
   • Choose whether to add a fixation after imaging
   • If fixation is enabled, define how long after imaging it occurs

   You can add multiple imaging sessions by clicking “+ Add imaging session” as many times as needed.

   The app automatically generates a unique Experiment ID following the pattern: YEAR_PROJECT_###.

3. Decide whether you want to schedule the experiment or keep it as an idea:
   • To schedule it, select an Anchor Date, which corresponds to the start of imaging of the first imaging session. (Don’t worry — this can be changed very easily later.) Then click “Add Experiment”.
   • To create an experiment idea only, clear the Anchor Date and click “Add to ideas”.
4. The planner automatically schedules:
   • Coating
   • Seeding
   • Imaging
   • Optional fixation and staining

   All steps are positioned relative to the anchor date and follow the experiment rules.

Once created, the experiment immediately appears in the calendar (or in the Ideas list if no date was set).

Before going further, a few core ideas are worth keeping in mind:

Anchor date
The anchor date defines the scheduled start of imaging of the first imaging session. All other steps are positioned relative to it.

Relative timing
When you move an experiment, its internal structure is preserved.

Imaging sessions and fixation
An experiment can have one or multiple imaging sessions, which are useful if you want to re-image a plate when different solutions have been added to the wells. For example a first imaging session could be ‘live experiment’ followed by fixation, then an immunostaining and a second imaging session. This will allow you to write information at the plate level for each of those session.

Nothing is blocked
Warnings and badges are informational only. The app never prevents actions.

Experiments, plates, and views
The Calendar, Experiments, Plates, and Imaging views are different lenses on the same underlying data.

Modifying an experiment

• Select an experiment from the calendar or the Experiments panel.
• Switch to Edit mode to update metadata or inter-block timing.
• Changes are immediately reflected everywhere.

To delete an experiment, use the Delete button in the selected experiment card.

Drag & drop behavior

• You can drag most blocks (seeding, imaging, fixation, staining) directly in the calendar.
• Dragging an experiment preserves all relative timings.
• Steps following a fixation can be moved freely without affecting the dates of the steps performed on live samples.

This makes rescheduling fast and safe.

Weekends and special days

• Weekends are automatically highlighted.
• Lab-wide special days (holidays, maintenance, retreats, etc.) can be defined in Settings.

These days are never blocked — they are visual planning signals only.

Warnings, badges, and capacity

The app can let you know if you more imaging are scheduled on a given instrument that the daily capacity of said instrument.

To enable this capacity warnings, you must define your imaging platforms and their daily plate capacity in Settings.

Once configured, the planner will automatically highlight days where the planned workload exceeds available capacity.

These warnings are informational and help anticipate overload. Hover over a badge to see details.

Plate maps are where you enter well level details of your experiment.

You can access plate maps:

• from the Plates view, or
• from the Imaging view by selecting an experiment and imaging session.

With plate maps you can:

• define structured fields (cell line, condition, antibody, etc.)
• visualize metadata directly on the plate
• copy and paste metadata across plates
• manage metadata per imaging session

Plate maps are tightly linked to experiments and imaging sessions, and are a key bridge between planning and data analysis.

Orchestra Planner focuses on planning and metadata structure.

To connect experiments with microscope image files, a companion tool called Metadata Extractor can be used:

• It reads microscope image files.
• It extracts acquisition metadata.
• It merges these data with experimental metadata from Orchestra Planner.
• It outputs a unified CSV file ready to be used in BioFile Finder (BFF).

This workflow makes it possible to search and filter large image datasets using rich experimental context.

• Orchestra Planner is a web app running locally in your browser.
• All data is stored locally, and exports are downloaded to your browser’s Downloads folder.
• The exported JSON file is the source of truth.

We recommend:

• creating a dedicated folder on your computer to store all Orchestra Planner JSON exports,
• keeping multiple versions to preserve history.

When importing data, the app can automatically:

• scan a folder containing multiple JSON files,
• detect and suggest the most recent version.

You can always bypass this and manually choose a different file if needed.

There is no cloud storage, no vendor lock-in, and backups are simple: copy your JSON files.

A full video tutorial walks through the complete workflow, from experiment creation to plate maps and data export.

🎥 Watch the full tutorial here:
(YouTube link will be embedded here)

The video complements this guide and is the recommended way to get started quickly.