faq.html

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<h1>
What is CellProfiler? FAQ
</h1>

<ul>
<li>
<a href="./examples.html#GetStarted">How do I get started?</a>
</li>

<li>
<a href=
"https://github.com/CellProfiler/CellProfiler/wiki/CellProfiler-release-notes">Where
can I find out more information about CellProfiler 2.1?</a>
</li>

<li>
<a href="#q1">Are CellProfiler and CellProfiler Analyst free?</a>
</li>

<li>
<a href="#q2">What is the difference between CellProfiler and
CellProfiler Analyst?</a>
</li>

<li>
<a href="#q3">Do CellProfiler and CellProfiler Analyst have to be
used together?</a>
</li>

<li>
<a href="#q4">How do I analyze my CellProfiler data?</a>
</li>

<li>
<a href="#q5">I'm an image processing expert. Why should I use
CellProfiler for development?</a>
</li>

<li>
<a href="#q6">I'm an image processing expert. Can I use
CellProfiler modules as part of a larger software package?</a>
</li>

<li>
<a href="#q7">What happened to the CellVisualizer software
project?</a>
</li>

<li>
<a href="#q8">I'm not a programmer. How much programming do I need
to know?</a>
</li>

<li>
<a href="#q9">I don't have MySQL. Can I use Microsoft Access?</a>
</li>

<li>
<a href="#q10">I have only a few images, should I use
CellProfiler?</a>
</li>

<li>
<a href="#q11">I have a small image set (20 images). Should I use
CellProfiler Analyst?</a>
</li>

<li>
<a href="#q13">Can I collaborate with you on a project?</a>
</li>

<li>
<a href="#q14">How can I show my enthusiasm for the CellProfiler
project and simultaneously help a good cause?</a>
</li>

<li>
<a href="#q15">What if I have more questions?</a>
</li>
</ul>

<h2>
<a name="q1">Are CellProfiler and CellProfiler Analyst free?</a>
</h2>

<p>
Yes. They are free and open source (GPL, some portions are also
BSD-licensed).
</p>

<h2>
<a name="q2">What is the difference between CellProfiler and
CellProfiler Analyst?</a>
</h2>

<p>
CellProfiler processes images and produces numerical data, which can
exported to Excel (if small) or deposited in files or exported to a
database (if large).
</p>

<p>
CellProfiler Analyst allows researchers to explore and analyze data.
The machine learning-based scoring of complex phenotypes is one
example of the analysis tools in CellProfiler Analyst.
</p>

<p>
<img alt=
"CellProfiler features include identification, measurement and hit picking"
border="0" height="383" src="http://d1zymp9ayga15t.cloudfront.net/images/FAQpageGraphic.gif" />
</p>

<h2>
<a name="q3">Do CellProfiler and CellProfiler Analyst have to be used
together?</a>
</h2>

<p>
No – while the two software packages work well together, they can be
used individually.
</p>

<h2>
<a name="q4">How do I analyze my CellProfiler data?</a>
</h2>

<p>
Please see our <a alt=
"Free Compatible Open Source Image Analysis Software" href=
"interfaces.html">Interfaces</a> page for a full listing of software
that can handle CellProfiler data, plus groups who we have partnered
with to expand analytical functionality.
</p>

<h2 id="q5">
I’m an image processing expert. Why should I use CellProfiler for
development?
</h2>

<p>
You can take advantage of the existing base of modules for the
mundane parts of image processing and focus on developing your own
algorithms or complex sequences of modules. When you have developed a
solution, you can contribute the code to the open-source CellProfiler
project, which saves you from writing your own GUI, compiling for
multiple platformsd, and answering basic questions from the public
(like installation troubleshooting and basic usage). Your method will
be widely available and in a format that biologists can actually use.
</p>

<p>
CellProfiler is written in Python, using Scipy and Numpy to implement
most of its algorithms. Concerned about speed? You can also wrap C or
Java code in Python, or use the Cython extension.
</p>

<p>
Check out our <a href="https://github.com/CellProfiler/CellProfiler/wiki">Developer
Wiki</a> for more information.
</p>

<h2 id="q6">
I'm an image processing expert. Can I use CellProfiler modules as
part of a larger software package?
</h2>

<p>
Sure! As long as you comply with the open-source <a href=
"https://raw.github.com/CellProfiler/CellProfiler/master/LICENSE">license</a>,
you can use pieces of the source code in your own software. For more
information about CellProfiler development, check out our <a href=
"https://github.com/CellProfiler/CellProfiler/wiki">Developer Wiki</a> and our <a href=
"interfaces.html#partners">Interfaces</a> page for examples of our
current partnerships.
</p>

<h2 id="q7">
What happened to the CellVisualizer software project?
</h2>

<p>
It was renamed <span style="font-weight:bold">CellProfiler
Analyst</span>.
</p>

<h2>
<a name="q8">I'm not a programmer. How much programming do I need to
know?</a>
</h2>

<p>
No programming experience is required to use either CellProfiler or
CellProfiler Analyst. CellProfiler Analyst can read data from CSV
files or MySQL databases; the latter might require some assistance
from your IT department to set up, but it's optional.
</p>

<h2>
<a name="q9">I don't have MySQL, can I use Microsoft Access?</a>
</h2>

<p>
You can also use Microsoft Access if you have fewer than 65,536 rows
per table (but each object in your analysis is a row), by exporting
the data as a CSV file using CellProfiler's ExportToExcel module or
data tool. Then, you can create various tables in Access, and use
another program (such as Excel) to analyze your data.
</p>

<h2>
<a name="q10">I have only a few images, should I use
CellProfiler?</a>
</h2>

<p>
Using CellProfiler lets you extract quantitative information from
your images, even if you only have a small number of them. However,
CellProfiler is designed to run on large image sets; there is more of
a payoff for large sets because the setup time for an analysis is
roughly the same whether you have 5 images or 500,000.
</p>

<h2>
<a name="q11">I have a small image set (20 images), should I use
CellProfiler Analyst?</a>
</h2>

<p>
For simple analyses of small image sets (creating plots or sorting
data by one particular measurement), it's probably more convenient to
use the built-in CellProfiler data tools or a spreadsheet program
like Excel after exporting your data with CellProfiler's
ExportToExcel module or data tool. CellProfiler Analyst is more
useful for large data sets or sophisticated analyses; it has several
built in features that will help you create histograms, scatterplots,
classify your data by a particular phenotype, and score your
classified results. CellProfiler Analyst is a great tool for data
exploration, especially if you need a simple-to-use program to help
you view your data in several formats.
</p>

<h2>
<a name="q13">Can I collaborate with you on a project?</a>
</h2>

<p>
Like most academic research groups, we must be very selective about
choosing research projects. We collaborate with academic and
commercial laboratories to solve challenging image analysis problems,
especially in high content screening, and in some cases we can
provide help for an hourly fee. Learn more and contact us via the
Carpenter lab <a href=
"http://www.broadinstitute.org/~anne/">website</a> to explore a
collaboration. You may also refer to our <a href=
"interfaces.html#partners">Interfaces</a> pages for projects where we
have partnered with other software groups to expand CellProfiler
functionality.
</p>

<h2>
<a name="q14">How can I show my enthusiasm for the CellProfiler
project and simultaneously help a good cause?</a>
</h2>

<p>
Go here: <a href="http://www.cafepress.com/CellProfiler">The
CellProfiler Shop</a>
</p>

<h2>
<a name="q15">What if I have more questions?</a>
</h2>

<p>
We suggest you visit the <a href=
"http://forum.cellprofiler.org">CellProfiler forum</a>.
</p>