For Olympus and Evident cellSens scans

Supercharge Your Lab's Quantification

CellLabel opens your .vsi files directly. Click cells to count them, or set up a node-based automated workflow. Export a clean spreadsheet directly from the app.

Download for Mac See features

Version 1.1.2 · Works on Apple Silicon and Intel Macs

CellLabel on a mouse midbrain section stained for TH: the samples list, the whole section with outlines around the left and right SNc and 73 TH+ points inside them, and the channel and class settings
Opens .vsi and .ets files Never changes your scans Exports CSV, TIFF, PNG and JSON Checks for updates on its own
How it works

Everything happens on one screen

The section you're counting stays in the middle of the window. Use the switch at the top right to move between Grid, Count and Export.

G

Grid

See every section in your project as a thumbnail. Pick a folder and CellLabel adds every .vsi file in it.

⇧1–9

Count

Click a cell to count it. ⌘-click to remove a point, or right-click to flag it for review.

⌘1

Detect

Let CellLabel find cells for you. Adjust the settings, check the results, then save them.

⌘2

Results

See one row per section and one column per class. Copy the table and paste it into Excel.

E

Export

Save each section as a PNG or TIFF image, along with your counts and a list of every point.

Try it

Automated Workflows

Detect finds cells in four steps. Channel picks the stain. Smooth blurs it so each cell becomes one bright spot. Find peaks marks every spot that is brighter than its surroundings by the amount you set. Label as keeps the spots inside your outline and counts them as a class. The panel below runs CellLabel's own code on a real stain, so change a number and press Run to see the result.

  • Nothing runs on its ownOpening a section or changing the pipeline doesn't start a run. You decide when to run it.
  • Preview any stepClick ◉ on a node to see its output on the image.
  • Undo in one stepCommitted points count the same as ones you clicked. ⌘Z removes the whole batch.
  • Reuse your settingsSave a pipeline as a template and use it on your next section.

This is the Detect panel running the app's own code on the SNc of a mouse midbrain section stained for TH, at quarter resolution. Drag a number or click ◉ to preview a step, then press Run. At the starting settings it finds 86 cells inside Reference 1.

The demo is easier to use on a larger screen.

Your data

Your scans and counts stay safe

Your scans are never changed

CellLabel only reads your .vsi and .ets files. Your points and settings are saved in a separate file.

Hourly backups

CellLabel backs up all your projects and points every hour. You can also save a full backup at any time.

Hiding doesn't delete anything

When you hide a layer, column or section, the counts are still there. Click Show all to bring them back.

Works with FIJI

TIFF exports are lossless and open directly in FIJI.

Download CellLabel

It works on Apple Silicon and Intel Macs. To get started, drag a folder of scans onto the window.

Download for Mac Version 1.1.2 · .dmg