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29 30 31 </head> 32 <body class="tex2jax_ignore purl-modifier-cellprofiler.org purl-provider_key- purl-value-1240 no-sidebars not-front path-node page-node-type-page has-glyphicons" ng-app="openscholar"> 33 <a href="#main-container" class="visually-hidden focusable skip-link"> 34 Skip to main content 35 </a> 36 37 <div id="page" class="dialog-off-canvas-main-canvas" data-off-canvas-main-canvas> 38 <header class="nav-bar navbar-defaults" id="navbar" role="banner"> 39 <div class="branding-header"> 40 <div class="container"> 41 <div class="region region-branding-header"> 42 43 44 45 </div> 46 47 <div class="mobile-menu"> 48 <button class="navbar-toggle main-menu" data-toggle="collapse" data-target="#navbar-collapse"> 49 <span class="sr-only">Toggle navigation</span> 50 <span class="glyphicon glyphicon-menu-hamburger"></span> 51 </button> 52 <button class="navbar-toggle secondary" data-target=".region-header-right #block-secondarymenu"> 53 <span class="sr-only">Toggle Secondary navigation</span> 54 <span class="glyphicon glyphicon-plus"></span></button> 55 <button class="navbar-toggle search" data-target=".region-header-right .block--type-search"> 56 <span class="sr-only">Toggle Search</span> 57 <span class="glyphicon glyphicon-search"></span> 58 </button> 59 </div> 60 </div> 61 </div> 62 <div class="header-container"> 63 <div class="container"> 64 <div class="row"> 65 <div class="col-sm-9 header-left"> 66 <div class="region region-header-left"> 67 68 <section id="block-block-content46be3f8d-46a6-4dab-b368-ddaf3455642a" class="block--type-custom-text-html block block-core block-block-content46be3f8d-46a6-4dab-b368-ddaf3455642a clearfix block-block-content" data-attr="custom_text_html"> 69 70 71 72 <div class="block-content"> 73 74 <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p><a href="http://cellprofiler.org/home"><img alt="CellProfiler Logo" class="media-element file-default" height="85" src="/files/files/cellprofiler/files/2017_11_21-cp_logo_black_tm_4.png" width="406"></a></p> 75</div> 76 77 </div> 78 79 </section> 80 81 82 </div> 83 84 </div> 85 <div class="header-right col-sm-3 pull-right"> 86 <div class="region region-header-right"> 87 88 89<section class="block block-core block-block-content858d1dbd-352b-4962-b0ba-c5987c3fbedf block-block-content block--type-search" id="block-block-content858d1dbd-352b-4962-b0ba-c5987c3fbedf" data-attr="search"> 90 91 92 93 <div class="block-content"> 94 <ul><li><form class="search-facets-widgets" data-drupal-selector="search-facets-widgets" role="search" action="" method="post" id="search-facets-widgets" accept-charset="UTF-8"> 95 <ul data-drupal-selector="edit-search"><li><div class="form-item js-form-item form-type-textfield js-form-type-textfield form-item-key-word js-form-item-key-word form-no-label form-group"> 96 <label for="edit-key-word" class="control-label sr-only js-form-required form-required">Search</label> 97 98 99 <input data-drupal-selector="edit-key-word" class="form-text required form-control" type="text" id="edit-key-word" name="key_word" value="" size="60" maxlength="128" required="required" aria-required="true" /> 100 101 102 103 </div> 104</li><li><div data-drupal-selector="edit-actions" class="form-actions form-group js-form-wrapper form-wrapper" id="edit-actions"><button data-drupal-selector="edit-submit" class="button button--primary js-form-submit form-submit btn-primary btn icon-before" type="submit" id="edit-submit" name="op" value="Search"><span class="icon glyphicon glyphicon-search" aria-hidden="true"></span> 105Search</button></div> 106</li></ul><input autocomplete="off" data-drupal-selector="form-lfea-o3e4dqkq7b5cmqdfw-up4fyls3eysprx1-gpju" type="hidden" name="form_build_id" value="form-Lfea-o3e4dqkq7b5CMQdfW_uP4FyLs3eysPRx1_gPjU" /><input data-drupal-selector="edit-search-facets-widgets" type="hidden" name="form_id" value="search_facets_widgets" /> 107</form> 108</li></ul> 109 </div> 110 </section> 111 112 </div> 113 114 </div> 115 </div> 116 </div> 117 </div> 118 <div id="navbar-collapse" class="navbar-collapse collapse"> 119 <div class="container"> 120 <div class="row"> <div class="region region-navigation-collapsible"> 121 122 123<nav role="navigation" aria-labelledby="block-primarymenu-menu" id="block-primarymenu"> 124 <div class="sr-only" id="block-primarymenu-menu">Primary menu</div> 125 126 127 128 <ul class="menu menu--group-menu-link-content-23 nav navbar-nav" > 129 <li class="first"> 130 <a href="https://cellprofiler.org/" title="">Home</a> 131 </li> 132 <li class="expanded dropdown active-trail"> 133 <a href="" aria-current="page" class="dropdown-toggle active-trail is-active" aria-expanded="false" aria-haspopup="true">Using CellProfiler <span class="caret"></span></a>
134 <a aria-hidden="true" class="dropmenu-child glyphicon glyphicon-plus"></a> 135 <ul class="dropdown-menu" > 136 <li class="first"> 137 <a href="https://cellprofiler.org/getting-started" data-drupal-link-system-path="node/1247">Getting Started</a> 138 </li> 139 <li class="active-trail"> 140 <a href="https://cellprofiler.org/examples" aria-current="page" class="active-trail is-active" data-drupal-link-system-path="node/1248">Examples</a> 141 </li> 142 <li> 143 <a href="https://tutorials.cellprofiler.org" title="">Tutorials</a> 144 </li> 145 <li class="last"> 146 <a href="https://cellprofiler.org/manuals" data-drupal-link-system-path="node/1250">Manuals</a> 147 </li> 148 </ul> 149 150 </li> 151 <li class="expanded dropdown"> 152 <a href="" class="dropdown-toggle" aria-expanded="false" aria-haspopup="true">About <span class="caret"></span></a> 153 <a aria-hidden="true" class="dropmenu-child glyphicon glyphicon-plus"></a> 154 <ul class="dropdown-menu" > 155 <li class="first"> 156 <a href="https://cellprofiler.org/about" data-drupal-link-system-path="node/1254">About CellProfiler</a> 157 </li> 158 <li> 159 <a href="https://cellprofiler.org/interfaces" data-drupal-link-system-path="node/1335">Software Interfaces and Partnerships</a> 160 </li> 161 <li> 162 <a href="https://cellprofiler.org/published-pipelines">Published Pipelines</a> 163 </li> 164 <li> 165 <a href="https://cellprofiler.org/impact" data-drupal-link-system-path="node/1336">Impact</a> 166 </li> 167 <li class="last"> 168 <a href="https://cellprofiler.org/citations" data-drupal-link-system-path="node/1253">Cite Us</a> 169 </li> 170 </ul> 171 172 </li> 173 <li class="expanded dropdown"> 174 <a href="" class="dropdown-toggle" aria-expanded="false" aria-haspopup="true">Support <span class="caret"></span></a> 175 <a aria-hidden="true" class="dropmenu-child glyphicon glyphicon-plus"></a> 176 <ul class="dropdown-menu" > 177 <li class="first"> 178 <a href="https://forum.image.sc/tag/cellprofiler">Forum</a> 179 </li> 180 <li> 181 <a href="https://cellprofiler.org/supportplan" data-drupal-link-system-path="node/1251">Custom Support</a> 182 </li> 183 <li class="last"> 184 <a href="https://cellprofiler.org/outreach" data-drupal-link-system-path="node/3790">Outreach</a> 185 </li> 186 </ul> 187 188 </li> 189 <li> 190 <a href="https://cellprofiler.org/releases" data-drupal-link-system-path="node/1246">Download</a> 191 </li> 192 <li> 193 <a href="http://carpenter-singh-lab.broadinstitute.org/blog" title="">Blog</a> 194 </li> 195 <li class="last"> 196 <a href="https://github.com/CellProfiler">GitHub</a> 197 </li> 198 </ul> 199 200 201 202 </nav> 203 204 </div> 205</div> 206 </div> 207 </div> 208 </header> 209 210 <div class="main-container container js-quickedit-main-content" id="main-container" tabindex="-1"> 211 <div class="row"> 212 213 <main role="main" id="content-column"> 214 <section class="col-sm-12"> 215 <div class="content-inner"> 216 <div class="region region-content"> 217 <div data-drupal-messages-fallback class="hidden"></div> <ol class="breadcrumb"> 218 <li > 219 <a href="https://cellprofiler.org/">Home</a> 220 </li> 221 <li > 222 Examples 223 </li> 224 </ol> 225 226 <h1 class="page-header page-title"> 227<span>Examples</span> 228</h1> 229 230 <article class="page full clearfix"> 231 232 233 234 235 236 <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> 241 242<h2> 243  244</h2> 245 246<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> 256 257</article> 258 259 260 <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"> 261 262 263 264 <div class="block-content"> 265 266 <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> 274 275 </div> 276 277 </section> 278 279 280 <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"> 281 282 283 284 <div class="block-content"> 285 <div class="layout layout--threecol-section layout--threecol-section--33-34-33"> 286 287 <div class="layout__region layout__region--first"> 288 289 <section class="block--type-custom-text-html block block-block-content block-block-content3c69f9f4-a1c8-4acc-8fd6-0bf59bf99251 clearfix" data-attr="custom_text_html"> 290 291 292 293 <div class="block-content"> 294 295 <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> 299 300 </div> 301 302 </section> 303 304 305 <section class="block--type-column block block-block-content block-block-content4464aeaa-37d4-4328-96fa-ab52eb4a829f clearfix" data-attr="column"> 306 307 308 309 <div class="block-content"> 310 <div class="layout layout--twocol-section layout--twocol-section--50-50"> 311 312 <div class="layout__region layout__region--first"> 313 314 <section class="block--type-embed-media block block-block-content block-block-contentf957
314d6ac-c875-45a4-a59c-4d37d282adbc clearfix" data-attr="embed_media"> 315 316 317 318 <div class="block-content"> 319 320<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" /> 322 323 </figure> 324 325 </div> 326 327 </section> 328 329 330 </div> 331 332 <div class="layout__region layout__region--second"> 333 334 <section class="block--type-embed-media block block-block-content block-block-content852879a1-802a-4436-bc4d-86857ef11fee clearfix" data-attr="embed_media"> 335 336 337 338 <div class="block-content"> 339 340<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> 344 345 </div> 346 347 </section> 348 349 350 </div> 351 352 </div> 353 354 </div> 355 356 </section> 357 358 359 <section class="block--type-custom-text-html block block-block-content block-block-content8f74dcf5-7807-44ba-b7c1-5e5119b62d8a clearfix" data-attr="custom_text_html"> 360 361 362 363 <div class="block-content"> 364 365 <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> 367 368 </div> 369 370 </section> 371 372 373 </div> 374 375 <div class="layout__region layout__region--second"> 376 377 <section class="block--type-custom-text-html block block-block-content block-block-content2fb4e99f-27cd-4a38-b8d4-deed5a6489d6 clearfix" data-attr="custom_text_html"> 378 379 380 381 <div class="block-content"> 382 383 <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;"> 384 <span style="color:#000000;">Fruit Fly cells</span> 385</h2> 386</div> 387 388 </div> 389 390 </section> 391 392 393 <section class="block--type-column block block-block-content block-block-contentc5498215-931f-4899-8ea3-e39a0fb16dee clearfix" data-attr="column"> 394 395 396 397 <div class="block-content"> 398 <div class="layout layout--twocol-section layout--twocol-section--50-50"> 399 400 <div class="layout__region layout__region--first"> 401 402 <section class="block--type-embed-media block block-block-content block-block-content7fa0f26f-4d69-4b35-846b-e104379e729d clearfix" data-attr="embed_media"> 403 404 405 406 <div class="block-content"> 407 408<figure class="os-widgets-embed-media-image"> 409 <img src="/files/cellprofiler/files/fruitflyimg_1.jpg" width="479" height="437" loading="lazy" class="img-responsive" /> 410 411 </figure> 412 413 </div> 414 415 </section> 416 417 418 </div> 419 420 <div class="layout__region layout__region--second"> 421 422 <section class="block--type-embed-media block block-block-content block-block-contente4e14304-203e-4297-acbd-e2b292cf902a clearfix" data-attr="embed_media"> 423 424 425 426 <div class="block-content"> 427 428<figure class="os-widgets-embed-media-image"> 429 <img src="/files/cellprofiler/files/fruitfly-coded_1.jpg" width="476" height="435" loading="lazy" class="img-responsive" /> 430 431 </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"> 584 585 586 587 <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 1026 <section class="block--type-custom-text-html block block-block-content block-block-contentb3c1579d-8afc-439b-b5bb-f56173d11abb clearfix" data-attr="custom_text_html"> 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> 1083 1084 </section> 1085 1086 1087 </div> 1088 1089 </div> 1090 1091 </div> 1092 1093 </section> 1094 1095 1096 <section class="block--type-custom-text-html block block-block-content block-block-content395e72aa-8bfd-4fbb-87e4-045a50b9dfec clearfix" data-attr="custom_text_html"> 1097 1098 1099 1100 <div class="block-content"> 1101 1102 <div class="prose field field--name-body field--type-text-with-summary field--label-hidden field--mode-full field--item"><p> 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> 1108 1109 </section> 1110 1111 1112 </div> 1113 1114 </div> 1115 1116 </div> 1117 1118 </section> 1119 1120 1121 <section id="block-block-contentb4780ef5-6e0a-48ed-bb77-680ee83b2f95" class="profiler-images block--type-column block block-core block-block-contentb4780ef5-6e0a-48ed-bb77-680ee83b2f95 clearfix block-block-content" data-attr="column"> 1122 1123 1124 1125 <div class="block-content"> 1126 <div class="layout layout--threecol-section layout--threecol-section--33-34-33"> 1127 1128 <div class="layout__region layout__region--first"> 1129 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"> 1131 1132 1133 1134 <div class="block-content"> 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"> 1147 1148 1149 1150 <div class="block-content"> 1151 <div class="layout layout--twocol-section layout--twocol-section--50-50"> 1152 1153 <div class="layout__region layout__region--first"> 1154 1155 <section class="block--type-embed-media block block-block-content block-block-content6a8899b2-513e-4f38-9369-4e7ac3220732 clearfix" data-attr="embed_media"> 1156 1157 1158 1159 <div class="block-content"> 1160 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> 1165 1166 </div> 1167 1168 </section> 1169 1170 1171 </div> 1172 1173 <div class="layout__region layout__region--second"> 1174 1175 <section class="block--type-embed-media block block-block-content block-block-content6ff221c5-a49b-4814-a968-af21347d3590 clearfix" data-attr="embed_media"> 1176 1177 1178 1179 <div class="block-content"> 1180 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> 1192 1193 </div> 1194 1195 </div> 1196 1197 </section> 1198 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> 1210 1211 </section> 1212 1213 1214 </div> 1215 1216 <div class="layout__region layout__region--second"> 1217 1218 <section class="block--type-custom-text-html block block-block-content block-block-contentc286eb29-0b2a-43de-a182-37bc910c5a90 clearfix" data-attr="custom_text_html"> 1219 1220 1221 1222 <div class="block-content"> 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"> 1235 1236 1237 1238 <div class="block-content"> 1239 <div class="layout layout--twocol-section layout--twocol-section--50-50"> 1240 1241 <div class="layout__region layout__region--first"> 1242 1243 <section class="block--type-embed-media block block-block-content block-block-contente05fa96b-d4ed-4fa8-953b-80c4c124f6c5 clearfix" data-attr="embed_media"> 1244 1245 1246 1247 <div class="block-content"> 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> 1253 1254 </div> 1255 1256 </section> 1257 1258 1259 </div> 1260 1261 <div class="layout__region layout__region--second"> 1262 1263 <section class="block--type-embed-media block block-block-content block-block-content4a9cc067-7ede-4bb8-a095-1e31da5dbddc clearfix" data-attr="embed_media"> 1264 1265 1266 1267 <div class="block-content"> 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> 1280 1281 </div> 1282 1283 </div> 1284 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> 1296 1297 </div> 1298 1299 </section> 1300 1301 1302 </div> 1303 1304 <div class="layout__region layout__region--third"> 1305 1306 <section class="block--type-custom-text-html block block-block-content block-block-contentda4abe61-b99d-4c8f-ab6b-001a9e07efaf clearfix" data-attr="custom_text_html"> 1307 1308 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"> 1323 1324 1325 1326 <div class="block-content"> 1327 <div class="layout layout--twocol-section layout--twocol-section--50-50"> 1328 1329 <div class="layout__region layout__region--first"> 1330 1331 <section class="block--type-embed-media block block-block-content block-block-contentbd88028a-2cde-4430-a090-fe74f3d3aff0 clearfix" data-attr="embed_media"> 1332 1333 1334 1335 <div class="block-content"> 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> 1343 1344 </section> 1345 1346 1347 </div> 1348 1349 <div class="layout__region layout__region--second"> 1350 1351 <section class="block--type-embed-media block block-block-content block-block-contentb3f82523-f6f4-43e3-a1f3-ddfdf292b51d clearfix" data-attr="embed_media"> 1352 1353 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 1378 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> 1393 1394 </div> 1395 1396 </div> 1397 1398 </section> 1399 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"> 1402 1403 1404 1405 <div class="block-content"> 1406 <div class="layout layout--threecol-section layout--threecol-section--33-34-33"> 1407 1408 <div class="layout__region layout__region--first"> 1409 1410 <section class="block--type-custom-text-html block block-block-content block-block-content59ec4755-7c84-45a3-b288-b781c117f2a2 clearfix" data-attr="custom_text_html"> 1411 1412 1413 1414 <div class="block-content"> 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"> 1427 1428 1429 1430 <div class="block-content"> 1431 <div class="layout layout--twocol-section layout--twocol-section--50-50"> 1432 1433 <div class="layout__region layout__region--first"> 1434 1435 <section class="block--type-embed-media block block-block-content block-block-content371df82e-f71c-46c0-b5ab-1160e7d5e024 clearfix" data-attr="embed_media"> 1436 1437 1438 1439 <div class="block-content"> 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> 1447 1448 </section> 1449 1450 1451 </div> 1452 1453 <div class="layout__region layout__region--second"> 1454 1455 <section class="block--type-embed-media block block-block-content block-block-content51141a52-6966-42dc-ab2f-7c77b137b133 clearfix" data-attr="embed_media"> 1456 1457 1458 1459 <div class="block-content"> 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> 1497 1498 <div class="layout__region layout__region--second"> 1499 1500 <section class="block--type-custom-text-html block block-block-content block-block-content49c6c560-4382-4a12-a862-005c9800a716 clearfix" data-attr="custom_text_html"> 1501 1502 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"> 1517 1518 1519 1520 <div class="block-content"> 1521 <div class="layout layout--twocol-section layout--twocol-section--50-50"> 1522 1523 <div class="layout__region layout__region--first"> 1524 1525 <section class="block--type-embed-media block block-block-content block-block-content51473ecf-c595-406b-ae34-10479f7e891e clearfix" data-attr="embed_media"> 1526 1527 1528 1529 <div class="block-content"> 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> 1537 1538 </section> 1539 1540 1541 </div> 1542 1543 <div class="layout__region layout__region--second"> 1544 1545 <section class="block--type-embed-media block block-block-content block-block-contenta3f43849-a8d2-4636-b694-6e5108174373 clearfix" data-attr="embed_media"> 1546 1547 1548 1549 <div class="block-content"> 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> 1580 1581 </div> 1582 1583 </section> 1584 1585 1586 </div> 1587 1588 <div class="layout__region layout__region--third"> 1589 1590 <section class="block--type-custom-text-html block block-block-content block-block-contentc7055830-b92f-4d78-80fa-45a20ae2c491 clearfix" data-attr="custom_text_html"> 1591 1592 1593 1594 <div class="block-content"> 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"> 1607 1608 1609 1610 <div class="block-content"> 1611 <div class="layout layout--twocol-section layout--twocol-section--50-50"> 1612 1613 <div class="layout__region layout__region--first"> 1614 1615 <section class="block--type-embed-media block block-block-content block-block-contentbad8bac7-b504-4b61-ab23-354810c25a4c clearfix" data-attr="embed_media"> 1616 1617 1618 1619 <div class="block-content"> 1620 1621<figure class="os-widgets-embed-media-image"> 1622 <img src="/files/cellprofiler/files/trackingexampleimg_1.gif" width="150" height="128" loading="lazy" class="img-responsive" /> 1623 1624 </figure> 1625 1626 </div> 1627 1628 </section> 1629 1630 1631 </div> 1632 1633 <div class="layout__region layout__region--second"> 1634 1635 <section class="block--type-embed-media block block-block-content block-block-content30fb986a-71ff-45ca-8867-b66b1e1661a9 clearfix" data-attr="embed_media"> 1636 1637 1638 1639 <div class="block-content"> 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> 1672 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 1692 <div class="layout__region layout__region--first"> 1693 1694 <section class="block--type-custom-text-html block block-block-content block-block-contentde808a7a-d2e5-451c-b2fd-d384ac39729d clearfix" data-attr="custom_text_html"> 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"> 1711 1712 1713 1714 <div class="block-content"> 1715 <div class="layout layout--twocol-section layout--twocol-section--50-50"> 1716 1717 <div class="layout__region layout__region--first"> 1718 1719 <section class="block--type-embed-media block block-block-content block-block-content8af5683d-b10d-4e08-ae5c-875d40714a5f clearfix" data-attr="embed_media"> 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"> 1765 1766 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> 1782 1783 </div> 1784 1785 </section> 1786 1787 1788 </div> 1789 1790 <div class="content-bottom"> 1791 <div class="region region-content-bottom"> 1792 1793 <section id="block-block-contentf60c57e2-0645-449b-8759-cd1b52f19bf3" class="block--type-custom-text-html block block-core block-block-contentf60c57e2-0645-449b-8759-cd1b52f19bf3 clearfix block-block-content" data-attr="custom_text_html"> 1794 1795 1796 1797 <div class="block-content"> 1798 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> 1802</div> 1803 1804 </div> 1805 1806 </section> 1807 1808 1809 </div> 1810 1811 </div> 1812 </div> 1813 </section> 1814 </main> 1815 1816 </div> 1817 </div> 1818 1819 <footer class="footer" role="contentinfo"> 1820 <div class="container"> 1821 <div class="row"> 1822 <div class="clearfix footer-middle"> 1823 <div class="col-sm-4">
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