https://cin-10.medizin.uni-tuebingen.de/eulerwiki/index.php?action=history&feed=atom&title=IgorIgor - Revision history2026-05-19T06:40:38ZRevision history for this page on the wikiMediaWiki 1.41.0https://cin-10.medizin.uni-tuebingen.de/eulerwiki/index.php?title=Igor&diff=133&oldid=prevJoesterle: /* Image preprocessing */2022-02-01T10:32:36Z<p><span dir="auto"><span class="autocomment">Image preprocessing</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:32, 1 February 2022</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** Load data with <code>ScanM/Load ScanM data file</code> ''…''</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** Load data with <code>ScanM/Load ScanM data file</code> ''…''</div></td></tr>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*** You can open <del style="font-weight: bold; text-decoration: none;">data </del>Data Browser under <code>Data/Data Browser</code></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*** You can open <ins style="font-weight: bold; text-decoration: none;">the </ins>Data Browser under <code>Data/Data Browser</code></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Process data with ''ScanM/Open OS GUI''</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Process data with ''ScanM/Open OS GUI''</div></td></tr>
</table>Joesterlehttps://cin-10.medizin.uni-tuebingen.de/eulerwiki/index.php?title=Igor&diff=122&oldid=prevJoesterle: Added instructions2022-02-01T09:56:48Z<p>Added instructions</p>
<p><b>New page</b></p><div>Igor is a licensed software used for recording and preprocessing of 2P data.<br />
<br />
In Igor you install software packages by putting them in the user folder, which is typically found here:<br />
<br />
<code>C:\Users\username\Documents\WaveMetrics\Igor Pro X User Files\, where x is the Igor version and username is your local username. These packages will be recompiled every time you open Igor.</code><br />
<br />
== Install Igor Pro ==<br />
<br />
# Ask Thomas for free license and the Igor version<br />
# Download the Igor for this license<br />
## <nowiki>https://www.wavemetrics.com/downloads/current</nowiki><br />
# Install plug-ins like SAFIRA and ScanM by following the readme here: https://github.com/eulerlab/ret_preproc<br />
## In Igor 8, you can get the HDF5 loader under ''Data/Load Waves/Packages/Install HDF5 Package''<br />
## Igor 9 should have this by default<br />
# You may need to install this https://www.wavemetrics.com/project/progresswindow<br />
## Unzip the file and copy it to the other *.ipf files in <code>...\Igor Pro X User Files\User Procedures</code><br />
## Create a link to this files and place it in <code>...\Igor Pro X User Files\Igor Procedures</code><br />
<br />
== Image preprocessing ==<br />
First install Igor Pro, ScanM and SAFIRA as described above. https://github.com/eulerlab/ret_preproc does also described how ScanM is to be used.<br />
<br />
* To process data recorded as .smp and .smh data pairs you<br />
** Load data with <code>ScanM/Load ScanM data file</code> ''…''<br />
** Select file in Data Browser and <code>Set Current Data Folder</code> (red arrow)<br />
*** You can open data Data Browser under <code>Data/Data Browser</code><br />
<br />
* Process data with ''ScanM/Open OS GUI''<br />
** Make New Parameter Table<br />
*** Most of the following should be detected automatically, but not TriggerMode which is stimulus dependent and is used to create snippets from the traces<br />
**** #26 TriggerMode = How many triggers per repetition. Here are some examples:<br />
***** Chirp: 2<br />
***** Moving Bar: 8<br />
***** Spotsize: 10<br />
***** DN: 1500<br />
**** #7 LightArtifact_cut = Columns for light artifact<br />
***** Setup 1: 1 and Setup 3: 3<br />
**** #8 Stimulator delay<br />
***** Setup 1: 64 and Setup 3: 75<br />
**** #23 Ignorse1stXsecond = Seconds to ignore<br />
*** Close Table<br />
*** ROI drawing with <code>Automated Cell Lab</code><br />
**** Margin left can be ignored or set to LightArtifact_cut<br />
**** Click add cell first, then draw<br />
**** When you are done click <code>Make SAFIRA Mask</code><br />
*** Close Menu window<br />
**** <code>Traces and Triggers</code><br />
**** <code>Export to create HD5 file that can be loaded in Python and DataJoint</code><br />
<br />
· Continue with next file</div>Joesterle