Browse — find the ideal starting time#

A time-course of plate scans is hard to skim one image at a time. The Timeline view of the Browse tab lays every source image out as a matrix — one row per plate (or folder / metadata group), one column per timepoint — so you can step across a single plate’s growth, compare plates side by side, and zoom into any one frame without leaving the page.

It builds on the single-image Browse viewer: same shared source root, same vendored OpenSeadragon deep-zoom, same ephemeral tile cache. The Timeline adds a folder/EXIF filmstrip by default, an optional per-axis source picker, token-keyed cached thumbnails, and a keyboard-driven focus-and-navigate matrix.

Step 1 - Switch Browse to Timeline mode#

Open the Browse tab, set a source root from the top bar (see Browse source images if you have not yet), then flip the Single ∣ Timeline toggle in the Browse header to Timeline:

The Browse tab in Timeline mode: the per-axis source controls, the focus window with one focused cell, the four edge navigation buttons, and the position readout.

By default the matrix uses the folder as the row axis and EXIF capture time as the time axis — a folder/EXIF filmstrip that needs no configuration. Capture time is read straight from each file’s EXIF block (no full-image decode), so even hundreds of source images lay out quickly.

Step 2 - Choose what drives each axis (optional)#

Two source selectors let you upgrade the default filmstrip:

  • Row source — folder (default), a {plate} pattern over the filename stems, or a metadata-CSV column.

  • Time source — exif (default), a {time} pattern, or a metadata-CSV column.

When you pick pattern, type a placeholder pattern such as {plate}_t{time} (with * wildcards and literal text). The compiled pattern extracts a plate identity and a time from each filename stem; an advanced-regex toggle switches the input to a raw regular expression requiring a named (?P<plate>…) group. A live pattern preview shows the per-stem captures so a mistyped pattern is visible before the matrix renders. Pattern rows stay folder-scoped — the same {plate} in two different folders is two separate rows.

When you pick csv, dropdowns choose the image-stem join column and the row/time value columns. The CSV joins folder-scoped by image stem (no path column), and a banner warns if a stem appears in more than one folder and so cannot be disambiguated. If no CSV is bound, a small nudge banner points you at the richer source picker.

Step 3 - Navigate the matrix#

The matrix is not scrollable. A centered, no-scroll window renders around one focused cell (highlighted), and the focused neighborhood plus a margin ring of just-off-screen cells mount their thumbnails — everything further out is offloaded, so the DOM stays light no matter how large the matrix is.

To move the focus:

  • Arrow keys — click the matrix viewport, then press ←/→ to walk one plate’s time-course and ↑/↓ to compare across plates. Focus clamps at the matrix edges (no wrap), and arrow keys are ignored while a text input (such as the pattern box) holds focus.

  • Edge buttons (◀▶▲▼) — the four on-edge directional buttons move the focus the same way for pointer-only use.

  • Position readout — a row N/M · time N/M caption reports where the focused cell sits in the matrix.

Stepping ←/→ across a row is how you find the ideal starting time — walk a plate’s frames until colonies are just resolvable, then read that column’s timepoint.

Each populated tile carries an N=k badge for the number of source images that resolved to that (row, time) cell, and a tile-size − / + stepper scales the whole matrix between a configured min and max.

Step 4 - Deep-zoom a single frame#

To inspect one frame at full resolution, open the deep-zoom pop-out:

The single-image deep-zoom pop-out opened from the focused cell, mounting an OpenSeadragon viewer that reuses the browse DZI route.

  • Press Enter (or Space) on the focused cell, or

  • hover any visible tile and click the revealed ⤢ button.

Either path opens the same pop-out modal and mounts an OpenSeadragon viewer that reuses the browse DZI deep-zoom route, so zoom and pan are GPU-smooth. Close the modal to return to the matrix with your focus unchanged.

Note

Thumbnails are token-keyed and cached under the same ephemeral tempfile.gettempdir()/phenotypic/browse tree as the single-view tiles (in a thumb/ sub-cache), wiped each session. RAW that cannot be decoded on the current platform surfaces an inline notice rather than a broken tile.

Where to next#

  • Browse source images — the single-image deep-zoom viewer the Timeline builds on.

  • Build a Pipeline — once you have picked a starting time, compose the pipeline that will process the run.