CellProfiler alternative
CellProfiler is free, open-source software for measuring cells and other objects in microscopy images, developed at the Broad Institute. It is widely used in academic labs and in high-content screening, and it is both loved and hated.
How does CellProfiler work?
You build an analysis as a pipeline: a sequence of modules that load images, identify objects such as nuclei and cells, measure them and export the results. Pipelines run on a desktop computer or, for large screens, on a computing cluster.
Where CellProfiler works well
CellProfiler runs on your own hardware, so it fits when your data policy rules out cloud processing entirely. It is the natural choice when you are reproducing a published CellProfiler pipeline and need to match it step for step. Because it is open source, developers building their own analysis methods in Python can change the software itself. And if you already have a validated pipeline and an expert to maintain it, there may be no reason to change.
Common problems
A steep learning curve
Choosing modules, thresholds and settings takes image analysis expertise, and a pipeline built for one assay rarely transfers to the next without tuning.
One person becomes the bottleneck
In many labs a single person builds and maintains the pipelines, and the work waits when they are busy or leave.
Results are separated from the images
Measurements are exported to spreadsheets or databases and explored in other tools, so checking a number against its cells takes extra steps.
What a good alternative looks like
For a cell-based assay that runs again and again, the analysis tool should:
- 1Let you build an analysis without pipeline or scripting expertise, while keeping every step visible and adjustable.
- 2Run the same analysis on every batch, whoever runs it.
- 3Keep results linked to the images, so any population can be checked against its cells.
- 4Share the full analysis with colleagues, not only exported tables.
- 5Run without local software or compute to install and maintain.
Cytely: built for repeated assays
Cytely is a cloud platform for reproducible cell-based microscopy assays, built on the data-driven microscopy approach published in Cell Reports Methods.
Workflows without pipeline expertise
Start from a ready assay, describe your assay to the AI workflow builder, or build visually. Every step has a live preview and stays editable.
A custom workflow at no cost
If your assay needs something new, our image analysis team builds the workflow for you, at no cost.
The same analysis every time
Save a versioned workflow and replicate the experiment on the next batch of images, whoever runs it.
Results linked to the cells
Gate populations on scatter plots, and the matching cells appear as crops and on an overview map of the sample.
Shared as a live analysis
Teammates work in the same datasets, and a link gives collaborators the interactive plots and gates, with no install or account.
Nothing to install or maintain
Cytely runs in the browser and processes the whole dataset in parallel in the cloud.
See how Cytely handles your assay
Questions
Does Cytely replace CellProfiler?
For repeated cell-based assays, many teams move that work into Cytely so more people can run it. The idea is familiar: a chain of analysis steps, but visual, in the cloud and linked to the results.
Do I need to write code?
No. Start from a ready assay, use the AI workflow builder, or build visually. If your assay needs something new, we build a custom workflow for you at no cost.
Can I use my results in other tools?
Yes. Export a CSV with every measurement for every detected object, including which gate each object falls in.
Is Cytely free?
There is a free plan, and paid plans for individuals and teams. See pricing.
Where is my data stored?
In Cytely's secure cloud. Cytely is ISO/IEC 27001 certified and data is encrypted in transit and at rest. See security.
Try it on your own images
Start free with your own data, or book a session and we will set up your assay with you.