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222                  Examples
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225
226    <h1 class="page-header page-title">
227<span>Examples</span>
228</h1>
229
230  <article class="page full clearfix">
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236  <div class="content">
237    
238            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2>
239	 
240</h2>
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242<h2>
243	 
244</h2>
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246<h2>
247	Previous Examples
248</h2>
249
250<p>
251	Previous examples (prior to 4.0) can be found on the <a href="/previous-examples" title="">previous examples</a> page, but we discourage their use because they are now outdated.
252</p>
253</div>
254      
255      </div>
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260  <section id="block-block-content2ce83f51-7ec1-4c46-a624-d3514fef5806" class="block--type-custom-text-html block block-core block-block-content2ce83f51-7ec1-4c46-a624-d3514fef5806 clearfix block-block-content" data-attr="custom_text_html">
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264      <div class="block-content">
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266            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2>
267	<span style="color:#000000;">CellProfiler example images and pipelines</span>
268</h2>
269
270<p>
271	Search the <a href="https://forum.image.sc/tag/cellprofiler" title="">online forum</a> for your application, check out others' <a href="http://cellprofiler.org/published-pipelines" title="">published pipelines</a>, or download our example pipelines and images below:
272</p>
273</div>
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276              
277  </section>
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280  <section id="block-block-contentf4ad0a69-686a-4cf7-9eaf-794d90300fc9" class="profiler-images block--type-column block block-core block-block-contentf4ad0a69-686a-4cf7-9eaf-794d90300fc9 clearfix block-block-content" data-attr="column">
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295            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
296	<span style="color:#000000;">Human cells</span>
297</h2>
298</div>
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320<figure class="os-widgets-embed-media-image">
321      <img src="/files/cellprofiler/files/humannuclei_3.jpg" width="512" height="512" loading="lazy" class="img-responsive" />
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340<figure class="os-widgets-embed-media-image">
341      <img src="/files/cellprofiler/files/humancolornucleism_2.jpg" width="512" height="512" loading="lazy" class="img-responsive" />
342
343    </figure>
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365            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p><span style="color:#000000;">Human HT29 cells are fairly smooth and elliptical. This pipeline demonstrates how to accurately identify these cells and how to measurements cellular parameters such as morphology, count, intensity and texture. </span><a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleHuman.zip">Download</a><span style="color:#000000;"> </span>(0.4 MB)</p>
366</div>
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384	<span style="color:#000000;">Fruit Fly cells</span>
385</h2>
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409      <img src="/files/cellprofiler/files/fruitflyimg_1.jpg" width="479" height="437" loading="lazy" class="img-responsive" />
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429      <img src="/files/cellprofiler/files/fruitfly-coded_1.jpg" width="476" height="435" loading="lazy" class="img-responsive" />
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431    </figure>
432
433      </div>
434              
435  </section>
436
437
438      </div>
439    
440  </div>
441
442      </div>
443              
444  </section>
445
446
447  <section class="block--type-custom-text-html block block-block-content block-block-contentce99feaa-3657-4cb8-9cf5-e87c2de59233 clearfix" data-attr="custom_text_html">
448    
449        
450    
451      <div class="block-content">
452        
453            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p><span style="color:#000000;">In contrast to the HT29 cells, Drosophila Kc167 cells are a highly textured and clumpy cell type. This pipeline demonstrates how to identify these clumpy cells and obtain morphological, intensity and texture measurements. </span><a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleFly.zip">Download</a><span style="color:#000000;"> </span>(4 MB)</p>
454</div>
455      
456      </div>
457              
458  </section>
459
460
461      </div>
462    
463          <div  class="layout__region layout__region--third">
464        
465  <section class="block--type-custom-text-html block block-block-content block-block-contented8b3258-9ac2-4acb-ae6c-c8aa6b538eaf clearfix" data-attr="custom_text_html">
466    
467        
468    
469      <div class="block-content">
470        
471            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
472	<span style="color:#000000;">Tumors</span>
473</h2>
474</div>
475      
476      </div>
477              
478  </section>
479
480
481  <section class="block--type-column block block-block-content block-block-contentf62f5222-6909-4b88-973e-8b12ce979f16 clearfix" data-attr="column">
482    
483        
484    
485      <div class="block-content">
486          <div class="layout layout--twocol-section layout--twocol-section--50-50">
487
488          <div  class="layout__region layout__region--first">
489        
490  <section class="block--type-embed-media block block-block-content block-block-content8df751dc-c6dd-41b8-be4b-fa690832f5b7 clearfix" data-attr="embed_media">
491    
492        
493    
494      <div class="block-content">
495        
496<figure class="os-widgets-embed-media-image">
497      <img src="/files/cellprofiler/files/exampletumorimg_5.png" width="400" height="300" loading="lazy" class="img-responsive" />
498
499    </figure>
500
501      </div>
502              
503  </section>
504
505
506      </div>
507    
508          <div  class="layout__region layout__region--second">
509        
510  <section class="block--type-embed-media block block-block-content block-block-contentbd08e260-9994-4c90-beb7-8c5e62900ab8 clearfix" data-attr="embed_media">
511    
512        
513    
514      <div class="block-content">
515        
516<figure class="os-widgets-embed-media-image">
517      <img src="/files/cellprofiler/files/exampletumorid_1.png" width="400" height="300" loading="lazy" class="img-responsive" />
518
519    </figure>
520
521      </div>
522              
523  </section>
524
525
526      </div>
527    
528  </div>
529
530      </div>
531              
532  </section>
533
534
535  <section class="block--type-custom-text-html block block-block-content block-block-contentb2c186da-7f17-49c0-ba09-0e96aa3341f5 clearfix" data-attr="custom_text_html">
536    
537        
538    
539      <div class="block-content">
540        
541            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p><span style="color:#000000;">A simple pipeline that identifies and counts tumors in a mouse lung, and then measures their size.</span> <a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleTumor.zip">Download</a> (0.9 MB)</p>
542</div>
543      
544      </div>
545              
546  </section>
547
548
549      </div>
550    
551  </div>
552
553      </div>
554              
555  </section>
556
557
558  <section id="block-block-content5a9276bf-588f-4348-98c1-ae0ec5ca4c11" class="profiler-images block--type-column block block-core block-block-content5a9276bf-588f-4348-98c1-ae0ec5ca4c11 clearfix block-block-content" data-attr="column">
559    
560        
561    
562      <div class="block-content">
563          <div class="layout layout--threecol-section layout--threecol-section--33-34-33">
564
565          <div  class="layout__region layout__region--first">
566        
567  <section class="block--type-custom-text-html block block-block-content block-block-contenta0c940f9-9a1d-4b1d-ba9a-1125dc4c19a0 clearfix" data-attr="custom_text_html">
568    
569        
570    
571      <div class="block-content">
572        
573            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
574	<span style="color:#000000;">Comet assay</span>
575</h2>
576</div>
577      
578      </div>
579              
580  </section>
581
582
583  <section class="block--type-column block block-block-content block-block-content578fd76f-f3c0-457f-ac1f-e6dd6f683a9c clearfix" data-attr="column">
584    
585        
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587      <div class="block-content">
588          <div class="layout layout--twocol-section layout--twocol-section--50-50">
589
590          <div  class="layout__region layout__region--first">
591        
592  <section class="block--type-embed-media block block-block-content block-block-content409515a8-56b1-4e05-85de-1e56254c1262 clearfix" data-attr="embed_media">
593    
594        
595    
596      <div class="block-content">
597        
598<figure class="os-widgets-embed-media-image">
599      <img src="/files/cellprofiler/files/examplecometimg_1.png" width="400" height="300" loading="lazy" class="img-responsive" />
600
601    </figure>
602
603      </div>
604              
605  </section>
606
607
608      </div>
609    
610          <div  class="layout__region layout__region--second">
611        
612  <section class="block--type-embed-media block block-block-content block-block-content325a0c24-4c95-4f2f-a528-f6b6095fadfd clearfix" data-attr="embed_media">
613    
614        
615    
616      <div class="block-content">
617        
618<figure class="os-widgets-embed-media-image">
619      <img src="/files/cellprofiler/files/examplecometid_4.png" width="400" height="300" loading="lazy" class="img-responsive" />
620
621    </figure>
622
623      </div>
624              
625  </section>
626
627
628      </div>
629    
630  </div>
631
632      </div>
633              
634  </section>
635
636
637  <section class="block--type-custom-text-html block block-block-content block-block-contentf8825761-ae0f-4e83-9d16-93ec3ec151fc clearfix" data-attr="custom_text_html">
638    
639        
640    
641      <div class="block-content">
642        
643            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p><span style="color:#000000;">This is a simple example of a DNA damage assay using single cell gel electrophoresis. Here, the measurement of interest is the length and intensity of the comet tail. Also, illumination correction is used to reduce background fluorescence prior to measurement. Also shown is a silver-stained comet example in which the percentage of DNA contained in the tail is calculated.</span> <a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleCometAssay.zip">Download</a> (0.4 MB)</p>
644</div>
645      
646      </div>
647              
648  </section>
649
650
651      </div>
652    
653          <div  class="layout__region layout__region--second">
654        
655  <section class="block--type-custom-text-html block block-block-content block-block-contentf5c48cfc-7e9e-46e8-a906-787eefcaba54 clearfix" data-attr="custom_text_html">
656    
657        
658    
659      <div class="block-content">
660        
661            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
662	Counting and scoring
663</h2>
664</div>
665      
666      </div>
667              
668  </section>
669
670
671  <section class="block--type-column block block-block-content block-block-content9df03a47-dd88-41da-a877-104080b640d1 clearfix" data-attr="column">
672    
673        
674    
675      <div class="block-content">
676          <div class="layout layout--twocol-section layout--twocol-section--50-50">
677
678          <div  class="layout__region layout__region--first">
679        
680  <section class="block--type-embed-media block block-block-content block-block-contente479679f-8c1d-4d56-86f5-f81d814fda16 clearfix" data-attr="embed_media">
681    
682        
683    
684      <div class="block-content">
685        
686<figure class="os-widgets-embed-media-image">
687      <img src="/files/cellprofiler/files/examplepercentposimg_1.png" width="128" height="128" loading="lazy" class="img-responsive" />
688
689    </figure>
690
691      </div>
692              
693  </section>
694
695
696      </div>
697    
698          <div  class="layout__region layout__region--second">
699        
700  <section class="block--type-embed-media block block-block-content block-block-content787c2f90-0be2-469b-8112-cc8671d2ea3e clearfix" data-attr="embed_media">
701    
702        
703    
704      <div class="block-content">
705        
706<figure class="os-widgets-embed-media-image">
707      <img src="/files/cellprofiler/files/examplepercentposid_1.png" width="128" height="128" loading="lazy" class="img-responsive" />
708
709    </figure>
710
711      </div>
712              
713  </section>
714
715
716      </div>
717    
718  </div>
719
720      </div>
721              
722  </section>
723
724
725  <section class="block--type-custom-text-html block block-block-content block-block-contentf77d831c-a6a2-4486-99e6-99f1774c237f clearfix" data-attr="custom_text_html">
726    
727        
728    
729      <div class="block-content">
730        
731            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p><span style="color:#000000;">Cell/particle counting and scoring the percentage of stained objects:  CellProfiler is commonly used to count cells or other objects as well as percent-positives, by measuring the per-cell staining intensity. This pipeline shows how to do both of these tasks, and demonstrates how various modules may be used to accomplish the same result.</span> <a href="https://cellprofiler-examples.s3.amazonaws.com/ExamplePercentPositive.zip">Download</a> (0.2 MB)</p>
732</div>
733      
734      </div>
735              
736  </section>
737
738
739      </div>
740    
741          <div  class="layout__region layout__region--third">
742        
743  <section class="block--type-custom-text-html block block-block-content block-block-content936fe37b-d908-4833-9a91-4996f6859718 clearfix" data-attr="custom_text_html">
744    
745        
746    
747      <div class="block-content">
748        
749            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
750	Yeast colony classification
751</h2>
752</div>
753      
754      </div>
755              
756  </section>
757
758
759  <section class="block--type-column block block-block-content block-block-content8fc3617e-92d7-42bd-8bbe-919d7c3c7aeb clearfix" data-attr="column">
760    
761        
762    
763      <div class="block-content">
764          <div class="layout layout--twocol-section layout--twocol-section--50-50">
765
766          <div  class="layout__region layout__region--first">
767        
768  <section class="block--type-embed-media block block-block-content block-block-contentb4784191-a412-4f25-9ecd-31b845bbf541 clearfix" data-attr="embed_media">
769    
770        
771    
772      <div class="block-content">
773        
774<figure class="os-widgets-embed-media-image">
775      <img src="/files/cellprofiler/files/yeastcrop_1.jpg" width="235" height="235" loading="lazy" class="img-responsive" />
776
777    </figure>
778
779      </div>
780              
781  </section>
782
783
784      </div>
785    
786          <div  class="layout__region layout__region--second">
787        
788  <section class="block--type-embed-media block block-block-content block-block-contente6d2c7b8-5f22-4a36-a86d-a4de8a7dea0e clearfix" data-attr="embed_media">
789    
790        
791    
792      <div class="block-content">
793        
794<figure class="os-widgets-embed-media-image">
795      <img src="/files/cellprofiler/files/yeastcropid_1.jpg" width="235" height="235" loading="lazy" class="img-responsive" />
796
797    </figure>
798
799      </div>
800              
801  </section>
802
803
804      </div>
805    
806  </div>
807
808      </div>
809              
810  </section>
811
812
813  <section class="block--type-custom-text-html block block-block-content block-block-content0222eaa0-fc3c-4225-952b-f9879139541e clearfix" data-attr="custom_text_html">
814    
815        
816    
817      <div class="block-content">
818        
819            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p><span style="color:#000000;">This pipeline demonstrates how to classify and count objects on the basis of their measured features. The example identifies uniformly round objects, in this case, yeast colonies growing on a dish. The pipeline also shows how to load a template and align it to a cropped image, as well as how to use illumination correction to subtract
819 for background illumination. </span><a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleYeastColonies.zip">Download</a> (0.6 MB) <br>
820<a href="/files/cellprofiler/files/85_Bray_CurrProtoMolBio_2015.pdf">Tutorial</a></p>
821</div>
822      
823      </div>
824              
825  </section>
826
827
828      </div>
829    
830  </div>
831
832      </div>
833              
834  </section>
835
836
837  <section id="block-block-contente69898f2-95b4-444d-b6a2-705c1d88d15f" class="profiler-images block--type-column block block-core block-block-contente69898f2-95b4-444d-b6a2-705c1d88d15f clearfix block-block-content" data-attr="column">
838    
839        
840    
841      <div class="block-content">
842          <div class="layout layout--threecol-section layout--threecol-section--33-34-33">
843
844          <div  class="layout__region layout__region--first">
845        
846  <section class="block--type-custom-text-html block block-block-content block-block-content2a630e07-dc55-444d-bf56-e2ba28a02837 clearfix" data-attr="custom_text_html">
847    
848        
849    
850      <div class="block-content">
851        
852            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
853	Yeast patch identification
854</h2>
855</div>
856      
857      </div>
858              
859  </section>
860
861
862  <section class="block--type-column block block-block-content block-block-content2153344b-d76e-45c1-aa9c-da670deb134e clearfix" data-attr="column">
863    
864        
865    
866      <div class="block-content">
867          <div class="layout layout--twocol-section layout--twocol-section--50-50">
868
869          <div  class="layout__region layout__region--first">
870        
871  <section class="block--type-embed-media block block-block-content block-block-content42307de0-a37d-4ba9-987a-3dd3ecc187e5 clearfix" data-attr="embed_media">
872    
873        
874    
875      <div class="block-content">
876        
877<figure class="os-widgets-embed-media-image">
878      <img src="/files/cellprofiler/files/exampleyeastpatch_1.png" width="156" height="160" loading="lazy" class="img-responsive" />
879
880    </figure>
881
882      </div>
883              
884  </section>
885
886
887      </div>
888    
889          <div  class="layout__region layout__region--second">
890        
891  <section class="block--type-embed-media block block-block-content block-block-content5ed67200-2567-467c-8b79-53c5412063c9 clearfix" data-attr="embed_media">
892    
893        
894    
895      <div class="block-content">
896        
897<figure class="os-widgets-embed-media-image">
898      <img src="/files/cellprofiler/files/exampleyeastpatchid_1.png" width="156" height="160" loading="lazy" class="img-responsive" />
899
900    </figure>
901
902      </div>
903              
904  </section>
905
906
907      </div>
908    
909  </div>
910
911      </div>
912              
913  </section>
914
915
916  <section class="block--type-custom-text-html block block-block-content block-block-content42d22937-5d27-4419-8575-59e2459b0c0b clearfix" data-attr="custom_text_html">
917    
918        
919    
920      <div class="block-content">
921        
922            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p>
923	<span style="color:#000000;">This pipeline identifies patches of yeast growing in a 96 well plate, serving as an introduction to the grid defintion and identification modules.</span> <a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleYeastPatches.zip" title="">Download</a> (0.5 MB)
924</p>
925</div>
926      
927      </div>
928              
929  </section>
930
931
932      </div>
933    
934          <div  class="layout__region layout__region--second">
935        
936  <section class="block--type-custom-text-html block block-block-content block-block-contentde254f34-256d-4a02-9baa-f8defb631bd4 clearfix" data-attr="custom_text_html">
937    
938        
939    
940      <div class="block-content">
941        
942            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
943	Tissue Neighbors
944</h2>
945</div>
946      
947      </div>
948              
949  </section>
950
951
952  <section class="block--type-column block block-block-content block-block-content8742d7a6-e9bb-4ec6-9912-376f47156cb1 clearfix" data-attr="column">
953    
954        
955    
956      <div class="block-content">
957          <div class="layout layout--twocol-section layout--twocol-section--50-50">
958
959          <div  class="layout__region layout__region--first">
960        
961  <section class="block--type-embed-media block block-block-content block-block-contente0289116-89e0-4483-b64d-6e4fdc8ebb86 clearfix" data-attr="embed_media">
962    
963        
964    
965      <div class="block-content">
966        
967<figure class="os-widgets-embed-media-image">
968      <img src="/files/cellprofiler/files/tissueneighbors_1.jpg" width="531" height="426" loading="lazy" class="img-responsive" />
969
970    </figure>
971
972      </div>
973              
974  </section>
975
976
977      </div>
978    
979          <div  class="layout__region layout__region--second">
980        
981  <section class="block--type-embed-media block block-block-content block-block-content293dcb8f-cce6-452a-b799-e30075830ed5 clearfix" data-attr="embed_media">
982    
983        
984    
985      <div class="block-content">
986        
987<figure class="os-widgets-embed-media-image">
988      <img src="/files/cellprofiler/files/clones1colorneighbors_1.jpg" width="531" height="426" loading="lazy" class="img-responsive" />
989
990    </figure>
991
992      </div>
993              
994  </section>
995
996
997      </div>
998    
999  </div>
1000
1001      </div>
1002              
1003  </section>
1004
1005
1006  <section class="block--type-custom-text-html block block-block-content block-block-content9b6abb3b-d182-4e52-bbf9-b92336d596ad clearfix" data-attr="custom_text_html">
1007    
1008        
1009    
1010      <div class="block-content">
1011        
1012            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p>
1013	<span style="color:#000000;">Tissue samples often have irregularly shaped cells with adjacent edges. This pipeline shows how to input a color tissue image, split it into 
1013its component channels, and then identify individual cells from a particular stain and record the number of neighbors that each cell has. </span><a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleNeighbors.zip" title="">Download</a> (0.9 MB)
1014</p>
1015</div>
1016      
1017      </div>
1018              
1019  </section>
1020
1021
1022      </div>
1023    
1024          <div  class="layout__region layout__region--third">
1025        
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1027    
1028        
1029    
1030      <div class="block-content">
1031        
1032            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
1033	Wound Healing
1034</h2>
1035</div>
1036      
1037      </div>
1038              
1039  </section>
1040
1041
1042  <section class="block--type-column block block-block-content block-block-contentcb959b66-5f3e-49ce-bb75-680f632035e6 clearfix" data-attr="column">
1043    
1044        
1045    
1046      <div class="block-content">
1047          <div class="layout layout--twocol-section layout--twocol-section--50-50">
1048
1049          <div  class="layout__region layout__region--first">
1050        
1051  <section class="block--type-embed-media block block-block-content block-block-content2b6f0ceb-78b5-4720-a967-5479b7a5bfeb clearfix" data-attr="embed_media">
1052    
1053        
1054    
1055      <div class="block-content">
1056        
1057<figure class="os-widgets-embed-media-image">
1058      <img src="/files/cellprofiler/files/wound-img_1.gif" width="255" height="170" loading="lazy" class="img-responsive" />
1059
1060    </figure>
1061
1062      </div>
1063              
1064  </section>
1065
1066
1067      </div>
1068    
1069          <div  class="layout__region layout__region--second">
1070        
1071  <section class="block--type-embed-media block block-block-content block-block-content07691ea2-0091-4eb0-8e9f-4f8356413432 clearfix" data-attr="embed_media">
1072    
1073        
1074    
1075      <div class="block-content">
1076        
1077<figure class="os-widgets-embed-media-image">
1078      <img src="/files/cellprofiler/files/wound-analysis_1.gif" width="255" height="170" loading="lazy" class="img-responsive" />
1079
1080    </figure>
1081
1082      </div>
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1091      </div>
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1103	<span style="color:#000000;">In this example, cells are grown as a tissue monolayer. Rather than identifying individual cells, this pipeline quantifies the area occupied by the tissue sample</span>. <a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleWoundHealing.zip" title="">Download</a> (1.2 MB)
1104</p>
1105</div>
1106      
1107      </div>
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1109  </section>
1110
1111
1112      </div>
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1116      </div>
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1120
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1130  <section class="block--type-custom-text-html block block-block-content block-block-content66323732-1d1e-46c2-b97b-de97dcffd3a0 clearfix" data-attr="custom_text_html">
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1135        
1136            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
1137	Illumination Correction
1138</h2>
1139</div>
1140      
1141      </div>
1142              
1143  </section>
1144
1145
1146  <section class="block--type-column block block-block-content block-block-contentf4c874fd-0d09-46a4-bd72-019248ceb1f8 clearfix" data-attr="column">
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1156    
1157        
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1159      <div class="block-content">
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1161<figure class="os-widgets-embed-media-image">
1162      <img src="/files/cellprofiler/files/exampleilluminationcorrection_orig_1.png" width="128" height="128" loading="lazy" class="img-responsive" />
1163
1164    </figure>
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1166      </div>
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1170
1171      </div>
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1176    
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1181<figure class="os-widgets-embed-media-image">
1182      <img src="/files/cellprofiler/files/exampleilluminationcorrection_corr_1.png" width="128" height="128" loading="lazy" class="img-responsive" />
1183
1184    </figure>
1185
1186      </div>
1187              
1188  </section>
1189
1190
1191      </div>
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1195      </div>
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1199
1200  <section class="block--type-custom-text-html block block-block-content block-block-content861cf09e-aa31-44aa-9ef8-d426a8f07a25 clearfix" data-attr="custom_text_html">
1201    
1202        
1203    
1204      <div class="block-content">
1205        
1206            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p><span style="color:#000000;">Illumination correction is often important for both accurate segmentation and for intensity measurements. This example shows how the CorrectIlluminationCalculate and CorrectIlluminationApply modules are used to compensate for the non-uniformities in illumination often present in microscopy images.</span> <a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleIlluminationCorrection.zip" title="">Download</a> (17.6 MB)<a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleIlluminationCorrection_Tutorial.pdf">
1206Tutorial</a></p>
1207</div>
1208      
1209      </div>
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1211  </section>
1212
1213
1214      </div>
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1223        
1224            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
1225	Colocalization
1226</h2>
1227</div>
1228      
1229      </div>
1230              
1231  </section>
1232
1233
1234  <section class="block--type-column block block-block-content block-block-content9e42c229-fbe9-4133-b804-b47116c92bd6 clearfix" data-attr="column">
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1244    
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1248        
1249<figure class="os-widgets-embed-media-image">
1250      <img src="/files/cellprofiler/files/examplecolocalization_orig_1.png" width="228" height="209" loading="lazy" class="img-responsive" />
1251
1252    </figure>
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1254      </div>
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1259      </div>
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1264    
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1268        
1269<figure class="os-widgets-embed-media-image">
1270      <img src="/files/cellprofiler/files/examplecolocalization_masked_1.png" width="228" height="209" loading="lazy" class="img-responsive" />
1271
1272    </figure>
1273
1274      </div>
1275              
1276  </section>
1277
1278
1279      </div>
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1281  </div>
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1283      </div>
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1285  </section>
1286
1287
1288  <section class="block--type-custom-text-html block block-block-content block-block-contenta7ae367b-0156-4679-ac92-a87610023d01 clearfix" data-attr="custom_text_html">
1289    
1290        
1291    
1292      <div class="block-content">
1293        
1294            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p><span style="color:#000000;">Measuring the colocalization between fluorescently labeled molecules is a widely used approach to measure the degree of spatial coincidence and potential interactions among subcellular species (e.g., proteins). This example shows how the object identifcation and RelateObjects modules are used to measure the degree of overlap between two fluorescent channels. </span><a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleColocalization.zip" title="">Download</a> (3.9 MB)<a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleColocalization_Tutorial.pdf">Tutorial</a></p>
1295</div>
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1297      </div>
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1300
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1309    
1310      <div class="block-content">
1311        
1312            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
1313	Human C-N translocation
1314</h2>
1315</div>
1316      
1317      </div>
1318              
1319  </section>
1320
1321
1322  <section class="block--type-column block block-block-content block-block-content6b442bb5-8ef4-4f30-a101-03893461e643 clearfix" data-attr="column">
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1332    
1333        
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1336        
1337<figure class="os-widgets-embed-media-image">
1338      <img src="/files/cellprofiler/files/examplevitraimg_1.png" width="240" height="249" loading="lazy" class="img-responsive" />
1339
1340    </figure>
1341
1342      </div>
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1346
1347      </div>
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1352    
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1354    
1355      <div class="block-content">
1356        
1357<figure class="os-widgets-embed-media-image">
1358      <img src="/files/cellprofiler/files/examplevitraid_1.png" width="240" height="249" loading="lazy" class="img-responsive" />
1359
1360    </figure>
1361
1362      </div>
1363              
1364  </section>
1365
1366
1367      </div>
1368    
1369  </div>
1370
1371      </div>
1372              
1373  </section>
1374
1375
1376  <section class="block--type-custom-text-html block block-block-content block-block-contentad7b915f-e8f9-41ef-93fe-8f39001841f7 clearfix" data-attr="custom_text_html">
1377    
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1379    
1380      <div class="block-content">
1381        
1382            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p>
1383	<span style="color:#000000;">In this human cytoplasm-nucleus translocation assay, learn how to load a previously calculated illumination correction function for two separate channels, measure protein content in the nucleus and cytoplasm, and calculate the ratio as a measure of translocation. This is a clumpy cell type, so studying the settings in primary object identification may be helpful for users interested in the more advanced options that module offers. More about these images can be found at the</span> <a href="http://www.broadinstitute.org/bbbc/BBBC014/">BBBC</a>. <a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleVitraImages.zip" title="">Download</a> (4.4 MB)
1384</p>
1385</div>
1386      
1387      </div>
1388              
1389  </section>
1390
1391
1392      </div>
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1394  </div>
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1396      </div>
1397              
1398  </section>
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1400
1401  <section id="block-block-content1c979586-8de9-4de2-a253-c42f3602a366" class="profiler-images block--type-column block block-core block-block-content1c979586-8de9-4de2-a253-c42f3602a366 clearfix block-block-content" data-attr="column">
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1415        
1416            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
1417	Imaging Flow Cytometry
1418</h2>
1419</div>
1420      
1421      </div>
1422              
1423  </section>
1424
1425
1426  <section class="block--type-column block block-block-content block-block-content05ffacc7-37d5-4cb2-8650-600fa06d29df clearfix" data-attr="column">
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1433          <div  class="layout__region layout__region--first">
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1436    
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1440        
1441<figure class="os-widgets-embed-media-image">
1442      <img src="/files/cellprofiler/files/imaging_flow_1_1.jpg" width="982" height="957" loading="lazy" class="img-responsive" />
1443
1444    </figure>
1445
1446      </div>
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1449
1450
1451      </div>
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1456    
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1458    
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1460        
1461<figure class="os-widgets-embed-media-image">
1462      <img src="/files/cellprofiler/files/imaging_flow_2_1.jpg" width="561" height="554" loading="lazy" class="img-responsive" />
1463
1464    </figure>
1465
1466      </div>
1467              
1468  </section>
1469
1470
1471      </div>
1472    
1473  </div>
1474
1475      </div>
1476              
1477  </section>
1478
1479
1480  <section class="block--type-custom-text-html block block-block-content block-block-contentdf756f7c-226a-4cb2-9860-f7568981914d clearfix" data-attr="custom_text_html">
1481    
1482        
1483    
1484      <div class="block-content">
1485        
1486            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p>
1487	<span style="color:#000000;">Imaging flow cytometry combines the high-throughput capabilities of conventional flow cytometry with single-cell imaging. CellProfiler can be used to analyze the resulting images from imaging flow cytometry, whether brightfield, darkfield, or fluorescence. The</span> <a href="http://cellprofiler.org/imagingflowcytometry" title="">IFC website</a> <span style="color:#000000;">page has further details on this workflow.</span> <br><a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleImagingFlowCytometryObjectsInGrid.zip" title="">Download</a> (21.2 MB)
1488</p>
1489</div>
1490      
1491      </div>
1492              
1493  </section>
1494
1495
1496      </div>
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1498          <div  class="layout__region layout__region--second">
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1503    
1504      <div class="block-content">
1505        
1506            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
1507	Speckle Counting
1508</h2>
1509</div>
1510      
1511      </div>
1512              
1513  </section>
1514
1515
1516  <section class="block--type-column block block-block-content block-block-content68b6418f-39d9-4767-a98f-c9dcbaae3cf8 clearfix" data-attr="column">
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1521          <div class="layout layout--twocol-section layout--twocol-section--50-50">
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1523          <div  class="layout__region layout__region--first">
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1530        
1531<figure class="os-widgets-embed-media-image">
1532      <img src="/files/cellprofiler/files/specklesab_1.gif" width="256" height="214" loading="lazy" class="img-responsive" />
1533
1534    </figure>
1535
1536      </div>
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1539
1540
1541      </div>
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1543          <div  class="layout__region layout__region--second">
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1550        
1551<figure class="os-widgets-embed-media-image">
1552      <img src="/files/cellprofiler/files/specklescd_1.gif" width="512" height="427" loading="lazy" class="img-responsive" />
1553
1554    </figure>
1555
1556      </div>
1557              
1558  </section>
1559
1560
1561      </div>
1562    
1563  </div>
1564
1565      </div>
1566              
1567  </section>
1568
1569
1570  <section class="block--type-custom-text-html block block-block-content block-block-content2e088b82-dc30-4b64-977b-5707698e4d6e clearfix" data-attr="custom_text_html">
1571    
1572        
1573    
1574      <div class="block-content">
1575        
1576            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p>
1577	<span style="color:#000000;">This pipeline shows how to identify smaller objects (foci) within larger objects (nuclei) and how to use the Relate module to establish a relationship between the two as well as perform per-object aggregate measurements (such as number of foci per nucleus). </span><a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleSpeckles.zip" title="">Download</a> (2.7 MB)
1578</p>
1579</div>
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1581      </div>
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1583  </section>
1584
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1595        
1596            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
1597	Object Tracking
1598</h2>
1599</div>
1600      
1601      </div>
1602              
1603  </section>
1604
1605
1606  <section class="block--type-column block block-block-content block-block-content48a581b5-6890-43b2-8e5f-6d62f77609db clearfix" data-attr="column">
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1616    
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1622      <img src="/files/cellprofiler/files/trackingexampleimg_1.gif" width="150" height="128" loading="lazy" class="img-responsive" />
1623
1624    </figure>
1625
1626      </div>
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1638    
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1640        
1641<figure class="os-widgets-embed-media-image">
1642      <img src="/files/cellprofiler/files/trackingexampleid_1.gif" width="150" height="128" loading="lazy" class="img-responsive" />
1643
1644    </figure>
1645
1646      </div>
1647              
1648  </section>
1649
1650
1651      </div>
1652    
1653  </div>
1654
1655      </div>
1656              
1657  </section>
1658
1659
1660  <section class="block--type-custom-text-html block block-block-content block-block-content078e6734-7a62-4eeb-85e2-6884f43db7c6 clearfix" data-attr="custom_text_html">
1661    
1662        
1663    
1664      <div class="block-content">
1665        
1666            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p>
1667	<span style="color:#000000;">This example shows an example of object tracking. This pipeline analyzes a time-lapse experiment to identify the cells and track them from frame to frame, which is challenging since the cells are also moving. In addition, this pipeline also extracts metadata from the filename and uses groups the images by metadata in order to independently process several sequences of images and output the measurements of each.</span> <a href="https://cellprofiler-examples.s3.amazonaws.com/ExampleTrackObjects.zip" title="">Download</a> (10 MB)
1668</p>
1669</div>
1670      
1671      </div>
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1673  </section>
1674
1675
1676      </div>
1677    
1678  </div>
1679
1680      </div>
1681              
1682  </section>
1683
1684
1685  <section id="block-block-content7b7ba05f-701f-480f-8c19-96cc9a7ae142" class="profiler-images block--type-column block block-core block-block-content7b7ba05f-701f-480f-8c19-96cc9a7ae142 
1685clearfix block-block-content" data-attr="column">
1686    
1687        
1688    
1689      <div class="block-content">
1690          <div class="layout layout--threecol-section layout--threecol-section--33-34-33">
1691
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1695    
1696        
1697    
1698      <div class="block-content">
1699        
1700            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2 style="text-align:center;">
1701	Worm Toolbox
1702</h2>
1703</div>
1704      
1705      </div>
1706              
1707  </section>
1708
1709
1710  <section class="block--type-column block block-block-content block-block-contentf15e0c80-36b5-4b31-ab54-4f63079e0bb9 clearfix" data-attr="column">
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1720    
1721        
1722    
1723      <div class="block-content">
1724        
1725<figure class="os-widgets-embed-media-image">
1726      <img src="/files/cellprofiler/files/worms_untangle_1.gif" width="424" height="411" loading="lazy" class="img-responsive" />
1727
1728    </figure>
1729
1730      </div>
1731              
1732  </section>
1733
1734
1735      </div>
1736    
1737          <div  class="layout__region layout__region--second">
1738        
1739  <section class="block--type-embed-media block block-block-content block-block-content7c843784-0101-4b48-a5e9-5a5e876a922a clearfix" data-attr="embed_media">
1740    
1741        
1742    
1743      <div class="block-content">
1744        
1745<figure class="os-widgets-embed-media-image">
1746      <img src="/files/cellprofiler/files/worms_untangle_output_1.gif" width="424" height="411" loading="lazy" class="img-responsive" />
1747
1748    </figure>
1749
1750      </div>
1751              
1752  </section>
1753
1754
1755      </div>
1756    
1757  </div>
1758
1759      </div>
1760              
1761  </section>
1762
1763
1764  <section class="block--type-custom-text-html block block-block-content block-block-content71778e17-61d5-4887-a573-2f3e67b19230 clearfix" data-attr="custom_text_html">
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1767    
1768      <div class="block-content">
1769        
1770            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item">These pipelines have been developed for high-throughput screens on <i>C. elegans</i> and extract measurements on a per-worm basis. The <a href="http://cellprofiler.org/wormtoolbox" title="">Worm Toolbox</a> page has further details on this workflow, as well as video tutorials, pipelines and image data.</div>
1771      
1772      </div>
1773              
1774  </section>
1775
1776
1777      </div>
1778    
1779    
1780    
1781  </div>
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1799            <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><h2>Previous Examples</h2>
1800
1801<p>Previous examples (prior to 4.0) can be found on the <a href="https://sites.broadinstitute.org/cellprofiler/previous-examples">previous examples</a> page, but we discourage their use because they are now outdated.</p>
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