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100.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<!-- See: http://trac.edgewall.org/wiki/TracInterfaceCustomization -->
<head>
<title>
#100 (Bio-Formats core library split)
– ImageJ
</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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<body>
<div id="main">
<div id="notice" style="width: 58em; max-width: 100%; margin-left: auto; margin-right: auto; border: 1px solid black; margin-bottom: 2em">
<table>
<tr>
<td style="font-size: 72px; color: firebrick; padding: 0 10px 0 10px">⚠</td>
<td>
<p style="margin: 0.4em">
NOTICE! This is a static HTML version of a legacy ImageJ Trac ticket.
</p>
<p style="margin: 0.4em">
The ImageJ project now
<a href="https://imagej.net/Issues">uses GitHub Issues</a> for issue tracking.
</p>
<p style="margin: 0.4em">
Please
<a href="https://github.com/imagej/imagej/issues/new">file all new issues</a>
there.
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</td>
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</div>
<div id="content" class="ticket">
<h1 id="trac-ticket-title">
<a href="100.html">Ticket #100</a>
<span class="status">(closed task: fixed)</span>
</h1>
<div id="ticket">
<div class="date">
<p>Opened 2010-06-22T12:04:13-05:00</p>
<p>Last modified 2013-06-07T15:37:54-05:00</p>
</div>
<h2 class="summary searchable">Bio-Formats core library split</h2>
<table class="properties">
<tr>
<th id="h_reporter">Reported by:</th>
<td headers="h_reporter" class="searchable">
curtis
</td>
<th id="h_owner">Owned by:</th>
<td headers="h_owner">
curtis
</td>
</tr>
<tr>
<th id="h_priority">
Priority:
</th>
<td headers="h_priority">
critical
</td>
<th id="h_milestone">
Milestone:
</th>
<td headers="h_milestone">
<strike>imagej2-b3-headless</strike>
</td>
</tr><tr>
<th id="h_component">
Component:
</th>
<td headers="h_component">
I/O
</td>
<th id="h_version">
Version:
</th>
<td headers="h_version">
</td>
</tr><tr>
<th id="h_severity">
Severity:
</th>
<td headers="h_severity">
non-issue
</td>
<th id="h_keywords">
Keywords:
</th>
<td headers="h_keywords" class="searchable">
</td>
</tr><tr>
<th id="h_cc">
Cc:
</th>
<td headers="h_cc" class="searchable">
</td>
<th id="h_blockedby">
Blocked By:
</th>
<td headers="h_blockedby">
<a class="closed" href="996.html" title="Standardize license blurbs in ImageJ2, ImgLib and SCIFIO/Bio-Formats">#996</a>
</td>
</tr><tr>
<th id="h_blocking">
Blocking:
</th>
<td headers="h_blocking">
<a class="closed" href="9.html" title="Redesign core I/O infrastructure">#9</a>, <a class="new" href="101.html" title="Update Bio-Formats in VisAD repository">#101</a>, <a class="closed" href="102.html" title="Contact ITK community regarding bf-core library split">#102</a>, <a class="new" href="1169.html" title="Update Bio-Formats downstream projects">#1169</a>, <a class="closed" href="1912.html" title="Redesign core I/O infrastructure [ndim-data]">#1912</a>
</td>
<th>
</th>
<td>
</td>
</tr>
</table>
<div class="description">
<h3 id="comment:description">
Description
<span class="lastmod" title="2012-03-29 19:22:39.275778+00:00">
(last modified by curtis)
</span>
</h3>
<div class="searchable">
<p>
Bio-Formats needs to be split into two halves: 1) SCIFIO: the core API, metadata handling and standard file format readers; and 2) Bio-Formats: the microscopy file format readers.<br />
</p>
<p>
The SCIFIO library will be BSD licensed, while Bio-Formats will remain GPL. This architecture will allow SCIFIO to become part of ImageJ2, as well as bundled with non-GPL libraries such as VisAD.<br />
</p>
</div>
</div>
</div>
<div>
<h2 class="foldable">Change History</h2>
<div id="changelog">
<div class="change" id="trac-change-1">
<h3 class="change">
<span class="threading">
<span id="comment:1" class="cnum">
<a href="#comment:1">comment:1</a>
</span>
</span>
Changed 2010-06-22T12:07:13-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Component</strong>
changed from <em>other</em> to <em>io</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-2">
<h3 class="change">
<span class="threading">
<span id="comment:2" class="cnum">
<a href="#comment:2">comment:2</a>
</span>
</span>
Changed 2010-07-20T14:59:34-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>biweekly-2010: Jul-12 to Jul-23</em> to <em>biweekly-2010: Jul-26 to Aug-06</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-3">
<h3 class="change">
<span class="threading">
<span id="comment:3" class="cnum">
<a href="#comment:3">comment:3</a>
</span>
</span>
Changed 2010-08-06T18:06:58-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>biweekly-2010: Jul-26 to Aug-06</em> to <em>biweekly-2010: Aug-09 to Aug-20</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-4">
<h3 class="change">
<span class="threading">
<span id="comment:4" class="cnum">
<a href="#comment:4">comment:4</a>
</span>
</span>
Changed 2010-09-15T11:57:42-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>biweekly-2010: Sep-07 to Sep-17</em> to <em>biweekly-2011: Jan-03 to Jan-14</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-5">
<h3 class="change">
<span class="threading">
<span id="comment:5" class="cnum">
<a href="#comment:5">comment:5</a>
</span>
</span>
Changed 2010-12-09T13:37:11-06:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Priority</strong>
changed from <em>major</em> to <em>critical</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-6">
<h3 class="change">
<span class="threading">
<span id="comment:6" class="cnum">
<a href="#comment:6">comment:6</a>
</span>
</span>
Changed 2011-02-15T09:34:14-06:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>biweekly-2011: Feb-14 to Feb-25</em> to <em>biweekly-2011: Feb-28 to Mar-11</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-7">
<h3 class="change">
<span class="threading">
<span id="comment:7" class="cnum">
<a href="#comment:7">comment:7</a>
</span>
</span>
Changed 2011-03-13T21:35:51-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>biweekly-2011: Feb-28 to Mar-11</em> to <em>biweekly-2011: Mar-14 to Mar-25</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-8">
<h3 class="change">
<span class="threading">
<span id="comment:8" class="cnum">
<a href="#comment:8">comment:8</a>
</span>
</span>
Changed 2011-03-28T10:41:11-05:00 by curtis
</h3>
<div class="comment searchable">
<p>
An initial split is committed to the bf-split branch. More work needs to be done to ensure things are working.<br />
</p>
</div>
</div>
<div class="change" id="trac-change-9">
<h3 class="change">
<span class="threading">
<span id="comment:9" class="cnum">
<a href="#comment:9">comment:9</a>
</span>
</span>
Changed 2011-03-28T10:41:24-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>biweekly-2011: Mar-14 to Mar-25</em> to <em>biweekly-2011: Mar-28 to Apr-08</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-10">
<h3 class="change">
<span class="threading">
<span id="comment:10" class="cnum">
<a href="#comment:10">comment:10</a>
</span>
</span>
Changed 2011-04-25T11:25:34-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>biweekly-2011: Apr-11 to Apr-22</em> to <em>biweekly-2011: May-23 to Jun-03</em>
</li>
</ul>
<div class="comment searchable">
<p>
Still no time for this yet. Will be needed eventually for ImageJ core I/O though.<br />
</p>
</div>
</div>
<div class="change" id="trac-change-11">
<h3 class="change">
<span class="threading">
<span id="comment:11" class="cnum">
<a href="#comment:11">comment:11</a>
</span>
</span>
Changed 2011-06-06T12:43:03-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>biweekly-2011: May-23 to Jun-03</em> to <em>biweekly-2011: Jun-20 to Jul-01</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-12">
<h3 class="change">
<span class="threading">
<span id="comment:12" class="cnum">
<a href="#comment:12">comment:12</a>
</span>
</span>
Changed 2011-07-27T14:50:23-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>biweekly-2011: Jul-18 to Jul-29</em> to <em>imagej-2.0-beta1</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-13">
<h3 class="change">
<span class="threading">
<span id="comment:13" class="cnum">
<a href="#comment:13">comment:13</a>
</span>
</span>
Changed 2011-10-18T14:43:40-05:00 by curtis
</h3>
<div class="comment searchable">
<p>
Initial version of the split is available in the scifio branch of bio-formats.git. The "scifio" component will be permissively licensed and provide the core I/O infrastructure, while the "bio-formats" component provides the proprietary file format (PFF) readers and is GPL-licensed.<br />
</p>
<p>
The OME team is planning to discuss the SCIFIO project on next Tuesday, October 25. The plan is to merge the scifio branch onto develop and master after that, then proceed with some major refactoring of the SCIFIO and Bio-Formats projects. But once the initial merge and relicensing is complete, this ticket can be closed.<br />
</p>
</div>
</div>
<div class="change" id="trac-change-14">
<h3 class="change">
<span class="threading">
<span id="comment:14" class="cnum">
<a href="#comment:14">comment:14</a>
</span>
</span>
Changed 2011-10-21T11:44:23-05:00 by curtis
</h3>
<div class="comment searchable">
<p>
See also <a class="ext-link" href="http://trac.openmicroscopy.org.uk/ome/intertrac/%237076" title="#7076 in OME Trac"><span class="icon"> </span>ome:#7076</a> for more on SCIFIO.<br />
</p>
</div>
</div>
<div class="change" id="trac-change-15">
<h3 class="change">
<span class="threading">
<span id="comment:15" class="cnum">
<a href="#comment:15">comment:15</a>
</span>
</span>
Changed 2011-11-01T10:46:36-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Status</strong>
changed from <em>new</em> to <em>accepted</em>
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-16">
<h3 class="change">
<span class="threading">
<span id="comment:16" class="cnum">
<a href="#comment:16">comment:16</a>
</span>
</span>
Changed 2011-11-18T12:18:30-06:00 by curtis
</h3>
<div class="comment searchable">
<p>
Yesterday, the scifio branch was <a class="ext-link" href="http://trac.openmicroscopy.org.uk/ome/intertrac/changeset%3A598e9d9/bioformats.git" title="changeset:598e9d9/bioformats.git in OME Trac"><span class="icon"> </span>merged to develop</a> and <a class="ext-link" href="http://trac.openmicroscopy.org.uk/ome/intertrac/changeset%3Aeaf971e/bioformats.git" title="changeset:eaf971e/bioformats.git in OME Trac"><span class="icon"> </span>then to master</a>. All that remains is to change the copyright blurbs.<br />
</p>
</div>
</div>
<div class="change" id="trac-change-17">
<h3 class="change">
<span class="threading">
<span id="comment:17" class="cnum">
<a href="#comment:17">comment:17</a>
</span>
</span>
Changed 2012-02-23T14:43:51-06:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Blocking</strong>
<em>9</em> added
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-18">
<h3 class="change">
<span class="threading">
<span id="comment:18" class="cnum">
<a href="#comment:18">comment:18</a>
</span>
</span>
Changed 2012-02-24T13:38:23-06:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Blocking</strong>
<em>102</em> added
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-19">
<h3 class="change">
<span class="threading">
<span id="comment:19" class="cnum">
<a href="#comment:19">comment:19</a>
</span>
</span>
Changed 2012-02-24T13:39:09-06:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Blocking</strong>
<em>101</em> added
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-18">
<h3 class="change">
<span class="threading">
<span id="comment:18" class="cnum">
<a href="#comment:18">comment:18</a>
</span>
</span>
Changed 2012-02-27T11:09:12-06:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Blocked By</strong>
<em>996</em> added
</li>
</ul>
<div class="comment searchable">
</div>
</div>
<div class="change" id="trac-change-19">
<h3 class="change">
<span class="threading">
<span id="comment:19" class="cnum">
<a href="#comment:19">comment:19</a>
</span>
</span>
Changed 2012-03-29T13:07:08-05:00 by curtis
</h3>
<ul class="changes">
<li>
<strong>Milestone</strong>
changed from <em>imagej-2.0-beta1</em> to <em>imagej-2.0-beta2</em>
</li>
</ul>
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<p>
Agreeing on the copyright blurb for SCIFIO is taking a very long time to sort out. Unfortunately, this ticket cannot be closed until that is done. Even though the split is done on the technical level, we cannot use SCIFIO as a separate BSD-licensed library in other tools (e.g., <a class="closed ticket" href="100.html#101" title="task: Bio-Formats core library split (closed: fixed)">VisAD</a> or <a class="closed ticket" href="100.html#102" title="task: Bio-Formats core library split (closed: fixed)">ITK</a>) until the license is fully sorted out.<br />
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<p>
For the ImageJ 2.0.0-beta1 release, we will need to add a blurb to the license explaining that while our intention is for the codebase to be BSD-licensed (and ImageJ2 itself is), the entire distribution is technically still a combined work licensed under GPLv2+, because of SCIFIO.<br />
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Changed 2012-03-29T14:22:39-05:00 by curtis
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Changed 2012-04-14T17:59:08-05:00 by curtis
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<p>
I have submitted <a class="ext-link" href="https://github.com/openmicroscopy/bioformats/pull/55"><span class="icon"> </span>a pull request</a> that updates the licenses for all Bio-Formats and SCIFIO components.<br />
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Changed 2012-05-14T10:18:47-05:00 by curtis
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Changed 2012-06-16T23:24:15-05:00 by curtis
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<p>
The license updates have now been merged to the develop branch.<br />
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Changed 2013-03-26T13:27:59-05:00 by curtis
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See also <a class="ext-link" href="http://trac.openmicroscopy.org.uk/ome/intertrac/%237405" title="#7405 in OME Trac"><span class="icon"> </span>OME #7405</a>.<br />
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Changed 2013-06-05T15:10:38-05:00 by bdezonia
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Changed 2013-06-07T15:37:54-05:00 by curtis
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<p>
(In <a class="closed ticket" href="9.html" title="feature: Redesign core I/O infrastructure (closed: fixed)">#9</a>) This ticket is really about improving the <em>infrastructure</em> if I/O for ImageJ2. With SCIFIO, we have now done that. The 2.0.0-beta-7 release is using SCIFIO 0.1.0—File Open and File Save are now extensible—so this ticket is complete.<br />
</p>
<p>
Remaining tickets about improving the existing I/O mechanism have been migrated to ticket <a class="closed ticket" href="1920.html" title="feature: Improve I/O support [analysis] (closed: moved)">#1920</a>.<br />
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