Compare Image Analysis Runs

Compare puts two or more image analysis runs into one data table, so treated reads against control in the same rows. You pick the runs, pick the measures they share, and the table arrives with its chart already open.

Building the Comparison

There are three ways in. Tick several runs on the Analysis tab and choose Compare on the bulk bar, use Compare in that tab's header, or open the ⋯ menu at the top of a run and choose Compare, which starts the dialog box with that run already picked. The header button appears once the project holds two runs with results, since two is the smallest comparison.

The first step is picking the runs. The funnel at the right end of the search box narrows a long list by Status, Edited, and, once more than one person has made a run, Created by. A run you have already picked stays visible whatever the filter says. With the search box empty the list stops at the 30 most recent, so type a name to reach an older one.

A run that can't join your picks stays in the list, dimmed, with the reason under its name. No results to compare yet means it has never run. No measure in common with your picks means its numbers and theirs share no column. Continue takes you to the second step, and Back returns you to the picks.

The second step opens on Measures to compare, with every shared measure ticked. Below it, Preview gives each group its image count and each measure's mean with a standard deviation, so you can read the comparison before you create it. If the compared images were acquired at different pixel sizes, a line above the preview flags it, because an area measured at one scale means something different at another.

Create data table builds it and lands you in Data Tables on a table with one row per image and a Group column naming each row's run, with the chart already open. The table is named after the runs it holds, or after their count once there are more than three.

Grouping by Condition, Timepoint, or Replicate

Group by starts on Each run and switches the comparison to Condition, Timepoint, or Replicate. Those three read the experiment design recorded on the images, so they stay grayed until the images carry it.

Label images, in that same step, opens a grid with a row per image and columns for Condition, Replicate, Timepoint, and Sort order. Type the labels in, or fill the whole grid at once from the filenames.

Under Fill from filenames, retype one of your names with {condition}, {replicate}, or {timepoint} where each label sits, and {*} for a part you don't need, such as a plate id or a date. The rest of the pattern has to match the name exactly. A pattern of {timepoint}_{condition}_r{replicate} reads t01_control_r1.tif, since the extension comes off before the match.

As you type, the line under the field says how many of your filenames fit and spells out what the pattern pulls from one of them, so you can see it works before Apply pattern fills the grid. A name the pattern doesn't fit keeps whatever labels it already has.

Every cell stays editable before you save. Sort order is the number a timepoint sorts by, so t9, t10, t11 land in that order along the axis. Filling from filenames takes that number from the first run of digits in the timepoint, and you can type over it. Save labels turns on the grouping you needed.

Reading the Result

A timepoint comparison keeps the course in its stored order, so a growth or closure curve reads left to right. Every other grouping sorts its groups alphabetically. Images with no label for the grouping you chose gather in an Unlabeled group at the end.

The comparison stays live the same way an embedded table does. When a source run's numbers change, the column header carries a dot reading Source data changed since last refresh, and Refresh from source in that column's menu pulls the new values in.

For error bars or a significance test, add the chart to a figure and use its Comparisons step, or run Compare groups from the table's Analyze menu, which is a t-test or ANOVA on a value column across groups. Data Tables covers the table itself, and Customize a Chart covers the chart.