Auto-Organotypic

1 The folder

A pull from an instrument, or anything this pipeline has already written. A tick means it holds a manifest, so the channels, wells and frame counts are read rather than guessed.

choose a folder

2 What is in it

What each recording would be outlined on, before anything is written. A recording with no matching channel is listed as not planned rather than dropped quietly.

Outline the channel a name (red, TRITC, Luc) or a one-based number

recording	field	axes	frames	channels	outline on

3 The run

Every setting here is a flag of auto_organotypic pipeline, with the same default. Nothing on this page can ask for something the command line cannot.

Stages

Before registration

Broad crop a coarse box around the tissue so registration works on a small frame. Off by default: it rewrites every stack it crops.

How much surround

Hand-drawn regions and given numbers

Answers used instead of the automatic method, for the recordings they match. One folder per step and not one for all of them: each step reads a different frame — the broad crop the raw recording, the outline the registered plane, the square crop the oriented canvas — and an ImageJ region does not record which frame it was drawn on. Draw on what the step sees.

Crops, drawn on the raw recordings

or the same box for every recording

Outlines, drawn on the outline plane

Which way is up, drawn base to tip

or the same angle for every recording Turn it over ImageJ's angle: 0 to the right, 90 straight up the screen, which is what Analyze > Measure reports for a line drawn from the ventral base to the dorsal tip.

Square crops, drawn on the oriented source

or the same square crop for every recording

A recording nobody drew

Pull from an instrument first

Leave empty when the folder is already pulled.

Experiment Instrument

Running

Write everything under

Recordings at once Include recordings a live pull has not finished

Carry on past a stage whose package is not installed

Dry run — resolve every stage and report what would happen

4 Progress

Each stage appears as it finishes. Stopping takes effect at the next stage boundary — a stage is one call into another package and cannot be interrupted part-way.