cellprofiler / examples Goto Github PK

Example CellProfiler pipelines.

License: BSD 3-Clause "New" or "Revised" License

Makefile 100.00%

examples's Introduction

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. More information can be found in the CellProfiler Wiki.

What version of CellProfiler should I use?

We recommend the stable release of CellProfiler.

You can download a stable release for macOS and Windows from the CellProfiler website.

If you’re contributing or planning to contribute to CellProfiler, you should compile CellProfiler from source. Instructions for compiling CellProfiler on Linux, macOS and Windows are available from CellProfiler’s GitHub wiki.

If you’re the maintainer of a third-party CellProfiler module, you should use the nightly release of CellProfiler. You can download a nightly release for macOS and Windows from the CellProfiler website. Let us know if we’ve inadvertently broken your module by submitting a GitHub issue.

If you’re an enthusiastic CellProfiler user, you should try the beta release of CellProfiler. You can download a beta release for macOS and Windows from the CellProfiler website. Let us know if you encounter a bug by submitting a GitHub issue.

examples's People

Contributors

Stargazers

Watchers

Forkers

karhohs annecarpenter minh-doan cclauss banzaiman histopathology mkcor qiujingtao philloidin stevemmarshall bdiazroh kimdesok echterobert zappapc

examples's Issues

Add ExampleFly pipeline.

Would it be possible to license the image data?

Hello,

I'm opening this issue in a context where I'd like to use one of the images found in ExampleHuman/. The license for this repo applies to the actual software.

Would it be possible to license the images explicitly? Using CC0 for example?

/cc @bethac07

Thank you very much,
Marianne

ExampleYeastColonies has a pipeline that demonstrates several IdentifyPrimaryObjects bugs

See CellProfiler/CellProfiler#2815

percent positive pipeline has bug in CalculateMath

The bug has been filed here CellProfiler/CellProfiler#2814

It has been disabled in the current pipeline, so after the bug is fixed it should be enabled.

Error in illumination correction example pipeline

There are 4 piplines in the example. In “ExampleIlluminationCorrection_Example1_AllMethod” pipeline it shows following error,
For reference CP version 3.1.8 & OS is ubuntu,

I request the concerned team to update the example pipeline in the webpage.
This issue is also with reference to a forum question,
https://forum.image.sc/t/error-while-processing-correctilluminationcalculate/30053/2

Colocalization error at CalculateMath

Bad in CP3: error at CalculateMath
Good in CP2.2: all is fine

Error messages:
ValueError: operands could not be broadcast together with shapes (1159,) (1573,)

ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Discussion on DefineGrid

The DefineGrid segmentation is heavily automated, in contrast to IdentifyPrimaryObjects that exposes many parameters. Is DefineGrid to specific? Do we have more test cases beyond this yeast patch example? I could see DefineGrid being simplified by looping an IdentifyPrimaryObjects module through the defined grid.

ExamplePercentHuman has omitted CalculateMath module due to a bug

Once the bug is fixed the pipeline should be updated. Alternatively, a short python script could also calculate this information.

Wound healing error at ExportToSpreadsheet

Bad in CP3: Error at ExportToSpreatsheet >> give .csv no values (only headers). If run headless, ends with error.
Good in CP2.2: all is fine

Error message: "The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()"

ExampleIlluminationCorrection_Example1_AllMethod error as SaveImages

Bad in CP3: Error at SaveImages TIFF 64-bit
Good in CP2.2: Save TIFF .mat just fine.
Error message:

ValueError: Images of type float must be between -1 and 1

Configure travis notifications.

ExampleUntangleWormsBrightfield is behaving differently between 2.2 and 3.0

From Minh's PR

Please review. The result from CP3.0 and CP2.2 is very much different.

Most importantly, at CorrectIlluminationCalculate :

In CP3.0, setting "Rescale the Illumination function" needs to be "Yes" for later modules to work, but still not as good in CP2.2
In CP2.2, setting "Rescale the Illumination function" = No >> result is good