Downloads of v 4.2.1:


Last Update:

23 Jul 2021

Package Maintainer(s):

Software Author(s):

  • Broad Institute


cellprofiler admin foss


  • 1
  • 2
  • 3

4.2.1 | Updated: 23 Jul 2021



Downloads of v 4.2.1:



Software Author(s):

  • Broad Institute

  • 1
  • 2
  • 3
CellProfiler 4.2.1

  • 1
  • 2
  • 3

All Checks are Passing

3 Passing Tests

Validation Testing Passed

Verification Testing Passed


Scan Testing Successful:

No detections found in any package files


To install CellProfiler, run the following command from the command line or from PowerShell:


To upgrade CellProfiler, run the following command from the command line or from PowerShell:


To uninstall CellProfiler, run the following command from the command line or from PowerShell:


NOTE: This applies to both open source and commercial editions of Chocolatey.

1. Ensure you are set for organizational deployment

Please see the organizational deployment guide

  • Open Source or Commercial:
    • Proxy Repository - Create a proxy nuget repository on Nexus, Artifactory Pro, or a proxy Chocolatey repository on ProGet. Point your upstream to Packages cache on first access automatically. Make sure your choco clients are using your proxy repository as a source and NOT the default community repository. See source command for more information.
    • You can also just download the package and push it to a repository Download

3. Enter your internal repository url

(this should look similar to

4. Choose your deployment method:

choco upgrade cellprofiler -y --source="'STEP 3 URL'" [other options]

See options you can pass to upgrade.

See best practices for scripting.

Add this to a PowerShell script or use a Batch script with tools and in places where you are calling directly to Chocolatey. If you are integrating, keep in mind enhanced exit codes.

If you do use a PowerShell script, use the following to ensure bad exit codes are shown as failures:

choco upgrade cellprofiler -y --source="'STEP 3 URL'"

Write-Verbose "Exit code was $exitCode"
$validExitCodes = @(0, 1605, 1614, 1641, 3010)
if ($validExitCodes -contains $exitCode) {
  Exit 0

Exit $exitCode

- name: Ensure cellprofiler installed
    name: cellprofiler
    state: present
    version: 4.2.1
    source: STEP 3 URL

See docs at

chocolatey_package 'cellprofiler' do
  action    :install
  version  '4.2.1'
  source   'STEP 3 URL'

See docs at

    Name: cellprofiler,
    Version: 4.2.1,
    Source: STEP 3 URL

Requires Otter Chocolatey Extension. See docs at

cChocoPackageInstaller cellprofiler
   Name     = 'cellprofiler'
   Ensure   = 'Present'
   Version  = '4.2.1'
   Source   = 'STEP 3 URL'

Requires cChoco DSC Resource. See docs at

package { 'cellprofiler':
  provider => 'chocolatey',
  ensure   => '4.2.1',
  source   => 'STEP 3 URL',

Requires Puppet Chocolatey Provider module. See docs at

salt '*' chocolatey.install cellprofiler version="4.2.1" source="STEP 3 URL"

See docs at

5. If applicable - Chocolatey configuration/installation

See infrastructure management matrix for Chocolatey configuration elements and examples.

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This package was approved as a trusted package on 23 Jul 2021.


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.

CellProfiler is designed to serve biologists as well as bioimage analysts who want a flexible system that is easy to deploy to collaborators who lack computational skills. It is commonly used for small-scale experiments involving a few images but is also routinely run on millions of images using cluster or cloud computing resources at some of the largest pharmaceutical companies and academic screening centers in the world.

We curate the overwhelming number of computer-vision algorithms to a small number that are robust, powerful, and well-suited to biological problems. We translate computer vision techniques into language familiar to biologists. The software uses a pipeline workflow, with modules that map to biologists’ goals. Once a pipeline is configured, most analyses are fully automated. We focus on components applicable to many biologists’ use cases rather than heavily customized to unique experimental setups. We provide sensible defaults, example pipelines, extensive documentation, and an active Q&A forum to get new users up and running quickly. We enable convenient workflows by making connections with other bioimaging software.


$ErrorActionPreference = 'Stop';

$packageName = 'cellprofiler'
$toolsDir = "$(Split-Path -parent $MyInvocation.MyCommand.Definition)"

$packageArgs = @{
  packageName    = $packageName
  unzipLocation  = $toolsDir
  fileType       = 'EXE'
  url            = ''
  validExitCodes = @(0)
  softwareName   = 'Cellprofiler*'
  checksum       = '1dab0892787b03d500eb4ac96848561459faace9588b22ab1bc08d4aaa6f6687'
  checksumType   = 'sha256'

Install-ChocolateyPackage @packageArgs
$ErrorActionPreference = 'Stop'

$packageName = 'cellprofiler'
$softwareName = 'CellProfiler*'
$installerType = 'EXE'
$validExitCodes = @(0)

$uninstalled = $false
$local_key = 'HKCU:\Software\Microsoft\Windows\CurrentVersion\Uninstall\*'
$machine_key = 'HKLM:\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\*'
$machine_key6432 = 'HKLM:\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Uninstall\*'

[array]$key = Get-ItemProperty -Path @($machine_key6432, $machine_key, $local_key) `
  -ErrorAction SilentlyContinue `
| Where-Object { $_.DisplayName -like "$softwareName" }

if ($key.Count -eq 1) {
  $key | ForEach-Object {
    $file = "$($_.UninstallString)"

    Uninstall-ChocolateyPackage -PackageName $packageName `
      -FileType $installerType `
      -SilentArgs "$silentArgs" `
      -ValidExitCodes $validExitCodes `
      -File "$file"
elseif ($key.Count -eq 0) {
  Write-Warning "$packageName has already been uninstalled by other means."
elseif ($key.Count -gt 1) {
  Write-Warning "$key.Count matches found!"
  Write-Warning "To prevent accidental data loss, no programs will be uninstalled."
  Write-Warning "Please alert package maintainer the following keys were matched:"
  $key | ForEach-Object { Write-Warning "- $_.DisplayName" }

Log in or click on link to see number of positives.

In cases where actual malware is found, the packages are subject to removal. Software sometimes has false positives. Moderators do not necessarily validate the safety of the underlying software, only that a package retrieves software from the official distribution point and/or validate embedded software against official distribution point (where distribution rights allow redistribution).

Chocolatey Pro provides runtime protection from possible malware.

Version Downloads Last Updated Status
CellProfiler 4.2.0 21 Friday, June 25, 2021 Exempted
CellProfiler 4.1.3 43 Wednesday, February 17, 2021 Approved
CellProfiler 4.0.7 32 Saturday, November 21, 2020 Approved
CellProfiler 4.0.6 37 Monday, October 19, 2020 Approved
CellProfiler 4.0.5 32 Friday, October 9, 2020 Approved

This package has no dependencies.

Discussion for the CellProfiler Package

Ground Rules:

  • This discussion is only about CellProfiler and the CellProfiler package. If you have feedback for Chocolatey, please contact the Google Group.
  • This discussion will carry over multiple versions. If you have a comment about a particular version, please note that in your comments.
  • The maintainers of this Chocolatey Package will be notified about new comments that are posted to this Disqus thread, however, it is NOT a guarantee that you will get a response. If you do not hear back from the maintainers after posting a message below, please follow up by using the link on the left side of this page or follow this link to contact maintainers. If you still hear nothing back, please follow the package triage process.
  • Tell us what you love about the package or CellProfiler, or tell us what needs improvement.
  • Share your experiences with the package, or extra configuration or gotchas that you've found.
  • If you use a url, the comment will be flagged for moderation until you've been whitelisted. Disqus moderated comments are approved on a weekly schedule if not sooner. It could take between 1-5 days for your comment to show up.
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