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369 | 369 | <ul class="md-nav__list"> |
370 | 370 |
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371 | 371 | <li class="md-nav__item"> |
372 | | - <a href="#convert" class="md-nav__link"> |
| 372 | + <a href="#iohub-convert" class="md-nav__link"> |
373 | 373 | <span class="md-ellipsis"> |
374 | 374 |
|
375 | 375 | convert |
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380 | 380 | </li> |
381 | 381 |
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382 | 382 | <li class="md-nav__item"> |
383 | | - <a href="#info" class="md-nav__link"> |
| 383 | + <a href="#iohub-info" class="md-nav__link"> |
384 | 384 | <span class="md-ellipsis"> |
385 | 385 |
|
386 | 386 | info |
|
391 | 391 | </li> |
392 | 392 |
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393 | 393 | <li class="md-nav__item"> |
394 | | - <a href="#rename-wells" class="md-nav__link"> |
| 394 | + <a href="#iohub-rename-wells" class="md-nav__link"> |
395 | 395 | <span class="md-ellipsis"> |
396 | 396 |
|
397 | 397 | rename-wells |
|
402 | 402 | </li> |
403 | 403 |
|
404 | 404 | <li class="md-nav__item"> |
405 | | - <a href="#set-scale" class="md-nav__link"> |
| 405 | + <a href="#iohub-set-scale" class="md-nav__link"> |
406 | 406 | <span class="md-ellipsis"> |
407 | 407 |
|
408 | 408 | set-scale |
|
987 | 987 | <ul class="md-nav__list"> |
988 | 988 |
|
989 | 989 | <li class="md-nav__item"> |
990 | | - <a href="#convert" class="md-nav__link"> |
| 990 | + <a href="#iohub-convert" class="md-nav__link"> |
991 | 991 | <span class="md-ellipsis"> |
992 | 992 |
|
993 | 993 | convert |
|
998 | 998 | </li> |
999 | 999 |
|
1000 | 1000 | <li class="md-nav__item"> |
1001 | | - <a href="#info" class="md-nav__link"> |
| 1001 | + <a href="#iohub-info" class="md-nav__link"> |
1002 | 1002 | <span class="md-ellipsis"> |
1003 | 1003 |
|
1004 | 1004 | info |
|
1009 | 1009 | </li> |
1010 | 1010 |
|
1011 | 1011 | <li class="md-nav__item"> |
1012 | | - <a href="#rename-wells" class="md-nav__link"> |
| 1012 | + <a href="#iohub-rename-wells" class="md-nav__link"> |
1013 | 1013 | <span class="md-ellipsis"> |
1014 | 1014 |
|
1015 | 1015 | rename-wells |
|
1020 | 1020 | </li> |
1021 | 1021 |
|
1022 | 1022 | <li class="md-nav__item"> |
1023 | | - <a href="#set-scale" class="md-nav__link"> |
| 1023 | + <a href="#iohub-set-scale" class="md-nav__link"> |
1024 | 1024 | <span class="md-ellipsis"> |
1025 | 1025 |
|
1026 | 1026 | set-scale |
@@ -1100,7 +1100,7 @@ <h2 id="iohub">iohub<a class="headerlink" href="#iohub" title="Permanent link">& |
1100 | 1100 | </tr> |
1101 | 1101 | </tbody> |
1102 | 1102 | </table> |
1103 | | -<h3 id="convert">convert<a class="headerlink" href="#convert" title="Permanent link">¶</a></h3> |
| 1103 | +<h3 id="iohub-convert">iohub convert<a class="headerlink" href="#iohub-convert" title="Permanent link">¶</a></h3> |
1104 | 1104 | <p>Converts Micro-Manager TIFF datasets to OME-Zarr</p> |
1105 | 1105 | <p><strong>Usage:</strong></p> |
1106 | 1106 | <div class="language-text highlight"><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>iohub convert [OPTIONS] |
@@ -1154,7 +1154,7 @@ <h3 id="convert">convert<a class="headerlink" href="#convert" title="Permanent l |
1154 | 1154 | </tr> |
1155 | 1155 | </tbody> |
1156 | 1156 | </table> |
1157 | | -<h3 id="info">info<a class="headerlink" href="#info" title="Permanent link">¶</a></h3> |
| 1157 | +<h3 id="iohub-info">iohub info<a class="headerlink" href="#iohub-info" title="Permanent link">¶</a></h3> |
1158 | 1158 | <p>View basic metadata of a list of FILES.</p> |
1159 | 1159 | <p>Supported formats are Micro-Manager-acquired TIFF datasets |
1160 | 1160 | (single-page TIFF, multi-page OME-TIFF, NDTIFF) |
@@ -1187,7 +1187,7 @@ <h3 id="info">info<a class="headerlink" href="#info" title="Permanent link">&par |
1187 | 1187 | </tr> |
1188 | 1188 | </tbody> |
1189 | 1189 | </table> |
1190 | | -<h3 id="rename-wells">rename-wells<a class="headerlink" href="#rename-wells" title="Permanent link">¶</a></h3> |
| 1190 | +<h3 id="iohub-rename-wells">iohub rename-wells<a class="headerlink" href="#iohub-rename-wells" title="Permanent link">¶</a></h3> |
1191 | 1191 | <p>Rename wells in an plate.</p> |
1192 | 1192 | <div class="language-text highlight"><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>iohub rename-wells -i plate.zarr -c names.csv |
1193 | 1193 | </span></code></pre></div> |
@@ -1229,7 +1229,7 @@ <h3 id="rename-wells">rename-wells<a class="headerlink" href="#rename-wells" tit |
1229 | 1229 | </tr> |
1230 | 1230 | </tbody> |
1231 | 1231 | </table> |
1232 | | -<h3 id="set-scale">set-scale<a class="headerlink" href="#set-scale" title="Permanent link">¶</a></h3> |
| 1232 | +<h3 id="iohub-set-scale">iohub set-scale<a class="headerlink" href="#iohub-set-scale" title="Permanent link">¶</a></h3> |
1233 | 1233 | <p>Update scale metadata in OME-Zarr datasets.</p> |
1234 | 1234 | <div class="language-text highlight"><pre><span></span><code><span id="__span-6-1"><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a>iohub set-scale -i input.zarr/*/*/* -t 1.0 -z 1.0 -y 0.5 -x 0.5 |
1235 | 1235 | </span></code></pre></div> |
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