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SBEM_scheme.html
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<!DOCTYPE html>
<html>
<style>
.render-table {
border:3px solid #C0C0C0;
border-collapse:collapse;
padding:28px;
font-size: 134%;
font-family: sans-serif
}
.render-table th {
border:3px solid #C0C0C0;
border-right: 4px solid #000;
color: #100080;
padding:28px;
background:#F0FDE0;
}
.render-table td {
border:3px solid #C0C0C0;
border-right: 4px solid #000;
padding:28px;
font-family: monospace;
}
i {
color: #FF00F0
}
tr:hover {background-color: #f5f5f5;}
</style>
<head>
<!-- this should be the modules URL -->
<base href="https://github.com/martinschorb/render-modules/blob/master/rendermodules/" target="_blank" rel="noopener">
</head>
<h2 style="text-align:center;padding:28px;font-family: sans-serif;border:3px solid #C0C0C0; border-radius: 25px">SBEMImage Alignment/Stitching routine</h2>
<table class="render-table">
<!-- <caption>Table 1</caption> -->
<thead>
<tr>
<th style="background:#F0CCCC">Processing</th>
<th>Input converter</th>
<th>generate MipMaps</th>
<th>Apply MipMaps to Render</th>
<th>Tilepair generation</th>
<th>Match features (SIFT)</th>
<th>Solve (2D or 3D depending on tilepairs)</th>
<th>Export to N5</th>
</tr>
</thead>
<tbody>
<!-- <tr>
<td style="font-family: sans-serif;background:#F3E3A0"> Metadata</td>
<td style="font-family: sans-serif;"> SBEMImage</td>
<td style="font-family: sans-serif;"> </td>
<td style="font-family: sans-serif;"> </td>
<td style="font-family: sans-serif;"> </td>
<td style="font-family: sans-serif;"> </td>
<td style="font-family: sans-serif;"> </td>
<td style="font-family: sans-serif;"> </td>
<td style="font-family: sans-serif;"> </td>
</tr> -->
<tr>
<td style="font-family: sans-serif;background:#F3E3A0"> Stack suffix</td>
<td> -</td>
<td> -</td>
<td> _mipmaps</td>
<td> _tp</td>
<td> no new stack, point matches are generated</td>
<td> _solved</td>
<td> output volume generated</td>
</tr>
<!-- <tr>
<td style="background:#F3E3A0"> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr> -->
<tr>
<td style="font-family: sans-serif;background:#F3E3A0"> Caller script</td>
<td> <a title="generate_EM_tilespecs_from_SBEMImage.py" href="dataimport/generate_EM_tilespecs_from_SBEMImage.py">generate_EM_tilespecs<wbr>_from_SBEMImage.py</a></td>
<td> <a title="generate_mipmaps.py" href="dataimport/generate_mipmaps.py">generate_mipmaps.py</a></td>
<td> <a title="apply_mipmaps_to_render.py" href="dataimport/apply_mipmaps_to_render.py">apply_mipmaps_to_render.py</a></td>
<td> <a title="create_tilepairs.py" href="pointmatch/create_tilepairs.py">create_tilepairs.py</a></td>
<td> <a title="generate_point_matches_spark.py" href="pointmatch/generate_point_matches_spark.py">generate_point_matches_spark.py</a></td>
<td> <a title="solve.py" href="solver/solve.py">solve.py</a></td>
<td> <a title="N5Client.java" href="https://github.com/saalfeldlab/render/blob/geometric_descriptor/render-ws-spark-client/src/main/java/org/janelia/render/client/spark/n5/N5Client.java"><i>N5Client.java</i></a></td>
</tr>
<tr>
<td style="font-family: sans-serif;background:#F3E3A0"> Parameters</td>
<td> <a title="GenerateSBEMTileSpecsParameters" href="dataimport/README.md#SBEM">GenerateSBEM<wbr>TileSpecsParameters</a></td>
<td> <a title="GenerateMipMapsParameters" href="dataimport/README.md#mipmaps">GenerateMipMapsParameters</a></td>
<td> <a title="AddMipMapsToStackParameters" href="dataimport/README.md#mipmaps2render">AddMipMapsToStackParameters</a></td>
<td> <a title="TilePairClientParameters" href="pointmatch/README.md#tilepairs">TilePairClientParameters</a> Can be 2D or 3D.</td>
<td> <a title="PointMatchClientParametersSpark" href="pointmatch/README.md#pm_spark">PointMatchClientParametersSpark</a></td>
<td> <a title="BigFetaSchema" href="https://bigfeta.readthedocs.io/en/latest/api/bigfeta/schemas.html">BigFetaSchema</a></td>
<td> see code</td>
</tr>
<tr>
<td style="font-family: sans-serif;background:#F3E3A0"> Client script</td>
<td> <a href="https://github.com/fcollman/render-python-apps">renderapi</a>.import_tilespecs, .create_stack -><a href="https://github.com/saalfeldlab/render/blob/master/docs/src/site/markdown/render-ws-java-client.md#import-json-client"><i>ImportJsonClient</i></a></td>
<td> None - Python-based (PIL). <a href="dataimport/create_mipmaps.py">dataimport.create_mipmaps_uri</a></td>
<td> <a href="https://github.com/AllenInstitute/render-python/tree/master/renderapi">renderapi</a>.resolvedtiles, .create_stack -><a href="https://github.com/saalfeldlab/render/blob/master/docs/src/site/markdown/render-ws-java-client.md#import-json-client"><i>ImportJsonClient</i></a></td>
<td> <a href="https://github.com/AllenInstitute/render-python/tree/master/renderapi/client/client_calls.py">renderapi.client</a>.tilePairClient -><a href="https://github.com/saalfeldlab/render/blob/master/docs/src/site/markdown/render-ws-java-client.md#tile-pair-client"><i>TilePairClient</i></a></td>
<td> <a href="https://github.com/saalfeldlab/render/blob/geometric_descriptor/render-ws-spark-client/src/main/java/org/janelia/render/client/spark/SIFTPointMatchClient.java"><i>SIFTPointMatchClient</i></a></td>
<td> <a title="BigFeta" href="https://bigfeta.readthedocs.io/en/latest/index.html">BigFeta</a></td>
<td> standalone</td>
</tr>
<tr>
<td style="font-family: sans-serif;background:#F3E3A0"> Parallelisation</td>
<td> mp.Pool in <a href="https://github.com/fcollman/render-python-apps">renderapi</a>.import_tilespecs</td>
<td> mp.Pool in <a title="generate_mipmaps.py" href="dataimport/generate_mipmaps.py">make_tilespecs_and_cmds</a></td>
<td> mp.Pool</td>
<td> <a href="https://github.com/AllenInstitute/render-python/tree/master/renderapi/client/client_calls.py">renderapi.client</a>.run_<b>subprocess</b>_mode</td>
<td> <a href="https://git.embl.de/schorb/volumealign/-/blob/master/spark_slurm.sh">spark on slurm</a></td>
<td> ??</td>
<td> <a href="https://git.embl.de/schorb/volumealign/-/blob/master/spark_slurm.sh">spark on slurm</a></td>
</tr>
<tbody>
</table>
</html>