Name: rapid analysis and exploration of fluorescence microscopy images
Uploaded: 2014-03-19T13:00:00
Description: Watch this Scientific Journal Video about Rapid Analysis and Exploration of Fluorescence Microscopy Images at JoVE.com

We thank Adam Coster and all other members of the Altschuler and Wu labs for helpful feedback and discussions. This research was supported by the National Institute of Health grants R01 GM085442 and CA133253 (S.J.A.), R01 GM081549 (L.F.W.), CPRIT RP10900 (L.F.W), and the Welch Foundation I-1619 (S.J.A.) and I-1644 (L.F.W.).

1. Preparing Samples and Imaging
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	<li>Cell culture
	<ol>
		<li>Split cultures routinely and maintain at 20-70% confluence. One day prior to the experiment, grow HeLa cells in DMEM (Dulbecco&#39;s Modified Eagle Medium, see Table of Materials) and supplemented with 10% FBS (Fetal Bovine Serum) and 1x penicillin/streptomycin.</li>
		<li>On day of experiment, split cells growing in culture (about 50% confluent).</li>
		<li>Wash cells with PBS (Phosphate Buffered Saline), expose to approximately 2 ml of trypsin/EDTA (...

<ol>
	<li>Collins, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ImageJ+for+microscopy.">ImageJ for microscopy.</a> Biotechniques. 43, 25-30 (2007).</li><li>Carpenter, A. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CellProfiler:+image+analysis+software+for+identifying+and+quantifying+cell+phenotypes.">CellProfiler: image analysis software for identifying and quantifying cell phenotypes.</a> Genome Biol. 7, (2006).</li><li>Shamir, L., Delaney, J. D., Orlov, N., Eckley, D. M., Goldberg, I. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pattern+Recognition+Software+and+Techniques+for+Biological+Image+Analysis.">Pattern Recognition Software and Techniques for Biological Image Analysis.</a> PLoS Comput. Biol. 6, (2010).</li><li>Rajaram, S., Pavie, B., Wu, L. F., Altschuler, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PhenoRipper:+software+for+rapidly+profiling+microscopy+images.">PhenoRipper: software for rapidly profiling microscopy images.</a> Nat. Methods. 9, 635-637 (2012).</li><li>Lundholt, B. K., Scudder, K. M., Pagliaro, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple+technique+for+reducing+edge+effect+in+cell-based+assays.">A simple technique for reducing edge effect in cell-based assays.</a> J. Biomol. Screen. 8, 566-570 (2003).</li><li>Slack, M. D., Martinez, E. D., Wu, L. F., Altschuler, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterizing+heterogeneous+cellular+responses+to+perturbations.">Characterizing heterogeneous cellular responses to perturbations.</a> Proc. Natl. Acad. Sci. U.S.A. 105, 19306-19311 (2008).</li><li>Wolf, D. E., Samarasekera, C., Swedlow, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+analysis+of+digital+microscope+images.">Quantitative analysis of digital microscope images.</a> Methods Cell. Biol. 81, 365-396 (2007).</li><li>Zwier, J. M., Van Rooij, G. J., Hofstraat, J. W., Brakenhoff, G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Image+calibration+in+fluorescence+microscopy.">Image calibration in fluorescence microscopy.</a> J Microsc. 216, 15-24 (2004).</li><li>Shamir, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wndchrm+-+an+open+source+utility+for+biological+image+analysis.">Wndchrm - an open source utility for biological image analysis.</a> Source Code Biol. Med. 3, 13 (2008).</li><li>Hamilton, N. A., Wang, J. T., Kerr, M. C., Teasdale, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Statistical+and+visual+differentiation+of+subcellular+imaging.">Statistical and visual differentiation of subcellular imaging.</a> BMC Bioinform. 10, 94 (2009).</li><li>Huang, K., Murphy, R. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+classification+of+subcellular+patterns+in+multicell+images+without+segmentation+into+single+cells.">Automated classification of subcellular patterns in multicell images without segmentation into single cells.</a> 2, 1139-1142 (2004).</li></ol>

The workflow described here allows fast and easy characterization and comparison of microscopy images. We first demonstrated how this workflow can help experiment optimization, for example by quickly performing quality control on microscopy images. Next, we demonstrated its potential for analyzing high-throughput screening data: we were able to group drugs based on their mechanism of action. The grouping of drugs was comparable to that found using more complex methods6, even though PhenoRipper was orders of ma...

Over the past decade, rapid advances in imaging technology have given many labs the ability to perform high-throughput microscopy. The challenge has now shifted from one of imaging to one of analysis. How can we characterize, compare, and explore the torrent of complex yet subtle phenotypes generated by a typical high-throughput imaging screen?
A number of image-analysis and informatics platforms have given users sophisticated toolboxes1-3 for extracting biological information from large collections of images. Yet many significant obstacles remain in analyzing data from high-throughput image-based screens. Difficulties involved with choosing appropriate characterizations of the images and fine tuning of algorithmic parameters (to the system of interest) often result in long setup times, particularly for users without image-analysis expertise. In particular, cell segmentation, the process of identifying individual cells in an image, is a major bottleneck in this regard. Segmentation can be highly sensitive to experimental parameters such as cell type, cell density and bio-markers, and frequently requires repeated adjustment for a large data set. For these reasons, image analysis is often an independent, terminal step performed by specialists rather than an integrated part of the experimental workflow. This precludes the rapid feedback cycle between analysis and experiment, a crucial part of assay development.
Here we describe an alternative workflow that is optimized for high-throughput fluorescence microscopy and avoids many of the aforementioned difficulties. To this end, we make use of PhenoRipper4, an open-source software platform for rapid exploration and analysis of microscopy images. Significantly, PhenoRipper avoids many of the challenges involved with cell segmentation by not attempting to identify single cells. Instead, PhenoRipper divides images into pixel blocks of subcellular size and characterizes images in terms of the blocks they contain. Specifically, PhenoRipper profiles blocks in terms of marker-colocalization-based features and automatically identifies4 the most representative block types in the training images. PhenoRipper then assigns to each block the most similar representative block type, and finally characterizes images based on the types of the blocks they contain.
Compared to more traditional single-cell-based approaches, this approach requires minimal fine tuning and expertise. As such, users only need to set two parameters: the block size and a threshold intensity (to discard noncellular portions of an image), both of which are set with graphical feedback. Importantly, the workflow described here has been shown4 to scale easily to much larger data sets, where the speed and minimal fine tuning provides large time and reliability gains. In practice, we find that this approach reduces the time required both for setup and running by multiple orders of magnitude4.
The primary output of PhenoRipper is a visual representation of image similarity, which enables the user to identify groups of experimental conditions that cause cells to display similar phenotypes. The groupings PhenoRipper finds typically have comparable &#34;biological interpretability&#34; to those generated by more time-consuming, cell-based methods4. In practice, this means that often, within half an hour of performing a typical 96-well fluorescence microscopy experiment, an experimenter without prior image-analysis experience can get a reliable readout about the performance of his or her experiment. The experimenter can then start exploring the relationships between different experimental conditions and relating these relationships to image phenotypes.
We demonstrate this workflow here by analyzing the effects of drugs in distinct mechanistic classes on HeLa cells stained for DNA and cytoskeletal markers. Images of cells treated with the same class of drugs were grouped together, and poor quality images (staining artifacts, out of focus cells and so on) appeared as outliers, making them easy to identify and potentially discard.
While this workflow is useful for a large number of image-based assays, there are clearly many situations where a different approach could potentially be more informative. For example, the output from PhenoRipper is primarily a relative comparison of fluorescence patterns across experimental conditions. If an absolute characterization of a specific single cell trait was required instead (for example the number of speckles in a cell), a single-cell-based analysis would be required. Nonetheless, even in this type of situation, PhenoRipper is likely to detect changes in these single-cell phenotypes and therefore be a useful tool for assay optimization.

<table border="0" cellpadding="0" cellspacing="0" width="855">
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		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DMEM, High Glucose</td>
			<td style="width:116px;">Invitrogen</td>
			<td align="right" style="width:119px;">11965</td>
			<td style="width:404px;">High Glucose, L-Glutamine</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:216px;"></td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:216px;">Marker Hoechst 33342</td>
			<td style="width:116px;">Invitrogen&#160;</td>
			<td style="width:119px;">H1399</td>
			<td style="width:404px;">DNA stain, dilution 1:2000 of 5mg/ml stock</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Marker phalloidin-Alexa488</td>
			<td style="width:116px;">Invitrogen&#160;</td>
			<td style="width:119px;">A12379</td>
			<td style="width:404px;">Conjugated phallotoxin, dilution 1:200</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Primary Antibody &#945;-tubulin</td>
			<td style="width:116px;">Sigma&#160;</td>
			<td style="width:119px;">T9026</td>
			<td style="width:404px;">Primary Ab, mouse monoclonal, dilution 1:200</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;width:216px;">Secondary Antivody anti-Mouse TRITC</td>
			<td style="width:116px;">Jackson&#160;</td>
			<td style="width:119px;">115-025-166</td>
			<td style="width:404px;">Conjugated secondary Ab, 0.5mg in 1ml PBS + 1ml glycerol</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:216px;">Aldosterone</td>
			<td></td>
			<td></td>
			<td style="width:404px;">concentration used :0.2 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Apicidin</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :20 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Colchicine</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.16 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Cortisol</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.2 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Dexamethasone</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.2 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Docetaxel</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.2 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">M344</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :20 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">MS-275</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :5 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Nocodazole</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.3 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Prednisolone</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.2 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">RU486</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.2 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Scriptaid</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :70 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Taxol</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.3 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Trichostatin A</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.2 &#956;M</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Vinorelbine</td>
			<td style="width:116px;"></td>
			<td style="width:119px;"></td>
			<td style="width:404px;">concentration used :0.3 &#956;M</td>
		</tr>
	</tbody>
</table>

rapid analysis and exploration of fluorescence microscopy images

Despite rapid advances in high-throughput microscopy, quantitative image-based assays still pose significant challenges. While a variety of specialized image analysis tools are available, most traditional image-analysis-based workflows have steep learning curves (for fine tuning of analysis parameters) and result in long turnaround times between imaging and analysis. In particular, cell segmentation, the process of identifying individual cells in an image, is a major bottleneck in this regard.
Here we present an alternate, cell-segmentation-free workflow based on PhenoRipper, an open-source software platform designed for the rapid analysis and exploration of microscopy images. The pipeline presented here is optimized for immunofluorescence microscopy images of cell cultures and requires minimal user intervention. Within half an hour, PhenoRipper can analyze data from a typical 96-well experiment and generate image profiles. Users can then visually explore their data, perform quality control on their experiment, ensure response to perturbations and check reproducibility of replicates. This facilitates a rapid feedback cycle between analysis and experiment, which is crucial during assay optimization. This protocol is useful not just as a first pass analysis for quality control, but also may be used as an end-to-end solution, especially for screening. The workflow described here scales to large data sets such as those generated by high-throughput screens, and has been shown to group experimental conditions by phenotype accurately over a wide range of biological systems. The PhenoBrowser interface provides an intuitive framework to explore the phenotypic space and relate image properties to biological annotations. Taken together, the protocol described here will lower the barriers to adopting quantitative analysis of image based screens.

Here we tested the ability of this workflow to group drugs based on their mechanism of action. HeLa cells were seeded in 30 wells of a 384-well plate and stained for DNA/actin/&#945;-tubulin. The specific primary antibodies, fluorescently-labeled secondary antibodies, and other fluorescent stains that were used are listed in Table of Materials. Wells were treated with 15 drugs belonging to three mechanistic classes (histone deacetylase inhibiting, microtubule targeting and DNA damaging) for 24 hr&#160;and imaged using an...

Watch this Scientific Journal Video about Rapid Analysis and Exploration of Fluorescence Microscopy Images at JoVE.com

Rapid Analysis and Exploration of Fluorescence Microscopy Images

Here we describe a workflow for rapidly analyzing and exploring collections of fluorescence microscopy images using PhenoRipper, a recently developed image-analysis platform.

Despite rapid advances in high-throughput microscopy, quantitative image-based assays still pose significant challenges. While a variety of specialized ...

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