Downloads:
1,114
Downloads of v 4.2.3:
59
Last Update:
11 Aug 2022
Package Maintainer(s):
Software Author(s):
- Broad Institute
Tags:
cellprofiler admin foss- Software Specific:
- Software Site
- Software Source
- Software License
- Software Docs
- Software Issues
- Package Specific:
- Package Source
- Package outdated?
- Package broken?
- Contact Maintainers
- Contact Site Admins
- Software Vendor?
- Report Abuse
- Download
CellProfiler
This is not the latest version of CellProfiler available.
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4.2.3 | Updated: 11 Aug 2022
- Software Specific:
- Software Site
- Software Source
- Software License
- Software Docs
- Software Issues
- Package Specific:
- Package Source
- Package outdated?
- Package broken?
- Contact Maintainers
- Contact Site Admins
- Software Vendor?
- Report Abuse
- Download
Downloads:
1,114
Downloads of v 4.2.3:
59
Maintainer(s):
Software Author(s):
- Broad Institute
CellProfiler 4.2.3
This is not the latest version of CellProfiler available.
Legal Disclaimer: Neither this package nor Chocolatey Software, Inc. are affiliated with or endorsed by Broad Institute. The inclusion of Broad Institute trademark(s), if any, upon this webpage is solely to identify Broad Institute goods or services and not for commercial purposes.
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Some Checks Have Failed or Are Not Yet Complete
Not All Tests Have Passed
Deployment Method: Individual Install, Upgrade, & Uninstall
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:
Deployment Method:
This applies to both open source and commercial editions of Chocolatey.
1. Enter Your Internal Repository Url
(this should look similar to https://community.chocolatey.org/api/v2/)
2. Setup Your Environment
1. Ensure you are set for organizational deployment
Please see the organizational deployment guide
2. Get the package into your environment
Option 1: Cached Package (Unreliable, Requires Internet - Same As Community)-
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 https://community.chocolatey.org/api/v2/. 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
-
Open Source
-
Download the package:
Download - Follow manual internalization instructions
-
-
Package Internalizer (C4B)
-
Run: (additional options)
choco download cellprofiler --internalize --version=4.2.3 --source=https://community.chocolatey.org/api/v2/
-
For package and dependencies run:
choco push --source="'INTERNAL REPO URL'"
- Automate package internalization
-
Run: (additional options)
3. Copy Your Script
choco upgrade cellprofiler -y --source="'INTERNAL REPO URL'" --version="'4.2.3'" [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="'INTERNAL REPO URL'" --version="'4.2.3'"
$exitCode = $LASTEXITCODE
Write-Verbose "Exit code was $exitCode"
$validExitCodes = @(0, 1605, 1614, 1641, 3010)
if ($validExitCodes -contains $exitCode) {
Exit 0
}
Exit $exitCode
- name: Install cellprofiler
win_chocolatey:
name: cellprofiler
version: '4.2.3'
source: INTERNAL REPO URL
state: present
See docs at https://docs.ansible.com/ansible/latest/modules/win_chocolatey_module.html.
chocolatey_package 'cellprofiler' do
action :install
source 'INTERNAL REPO URL'
version '4.2.3'
end
See docs at https://docs.chef.io/resource_chocolatey_package.html.
cChocoPackageInstaller cellprofiler
{
Name = "cellprofiler"
Version = "4.2.3"
Source = "INTERNAL REPO URL"
}
Requires cChoco DSC Resource. See docs at https://github.com/chocolatey/cChoco.
package { 'cellprofiler':
ensure => '4.2.3',
provider => 'chocolatey',
source => 'INTERNAL REPO URL',
}
Requires Puppet Chocolatey Provider module. See docs at https://forge.puppet.com/puppetlabs/chocolatey.
4. 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 11 Aug 2022.
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'
$softwareName = 'CellProfiler*'
$installerType = 'EXE'
$silentArgs = '/VERYSILENT /NORESTART /NOCANCEL'
$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.
- cellprofiler.4.2.3.nupkg (06539617b9a5) - ## / 62
- CellProfiler-Windows-4.2.3.exe (8793645d3408) - ## / 51
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.
Add to Builder | Version | Downloads | Last Updated | Status |
---|---|---|---|---|
CellProfiler 4.2.8 | 41 | Wednesday, September 18, 2024 | Approved | |
CellProfiler 4.2.7 | 29 | Tuesday, July 30, 2024 | Approved | |
CellProfiler 4.2.6 | 95 | Tuesday, August 15, 2023 | Approved | |
CellProfiler 4.2.5 | 120 | Monday, December 19, 2022 | Approved | |
CellProfiler 4.2.4 | 71 | Friday, August 12, 2022 | Approved | |
CellProfiler 4.2.3 | 59 | Thursday, August 11, 2022 | Approved | |
CellProfiler 4.2.1 | 148 | Friday, July 23, 2021 | Approved | |
CellProfiler 4.2.0 | 93 | Friday, June 25, 2021 | Exempted | |
CellProfiler 4.1.3 | 122 | Wednesday, February 17, 2021 | Approved | |
CellProfiler 4.0.7 | 113 | Saturday, November 21, 2020 | Approved | |
CellProfiler 4.0.6 | 103 | Monday, October 19, 2020 | Approved | |
CellProfiler 4.0.5 | 120 | Friday, October 9, 2020 | Approved |
This package has no dependencies.
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.