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        <title>Data Analysis — CLARITY forum</title>
        <link>https://forum.claritytechniques.org/</link>
        <pubDate>Sat, 08 Aug 2026 01:11:30 +0000</pubDate>
        <language>en</language>
            <description>Data Analysis — CLARITY forum</description>
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        <title>Whole/ Half brain analysis</title>
        <link>https://forum.claritytechniques.org/discussion/211/whole-half-brain-analysis</link>
        <pubDate>Thu, 25 Oct 2018 06:52:31 +0000</pubDate>
        <category>Data Analysis</category>
        <dc:creator>GabLin</dc:creator>
        <guid isPermaLink="false">211@/discussions</guid>
        <description><![CDATA[Dear all,

I soon have to start an analysis of half and whole mice cleared brain with RNA signal. Do you have any suggestion about what s might be the best software (arivis, imaris, clear map ecc.) to perform a density quantification and connectivity analysis.


Thanks

Gab
]]>
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    <item>
        <title>Processing of Data</title>
        <link>https://forum.claritytechniques.org/discussion/208/processing-of-data</link>
        <pubDate>Mon, 11 Jun 2018 08:30:15 +0000</pubDate>
        <category>Data Analysis</category>
        <dc:creator>Fabio</dc:creator>
        <guid isPermaLink="false">208@/discussions</guid>
        <description><![CDATA[Hi everyone,

if you looking for possibilities to process your large dataasets (illumination selection, stitching, multiple angle registration, fusion, deconvolution) check the BigStitcher Fiji plugin.

https://www.biorxiv.org/content/early/2018/06/10/343954.full.pdf+html]]>
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    <item>
        <title>Raw data of the rat entorhinal cortex and hippocampus?</title>
        <link>https://forum.claritytechniques.org/discussion/141/raw-data-of-the-rat-entorhinal-cortex-and-hippocampus</link>
        <pubDate>Mon, 15 Dec 2014 09:50:21 +0000</pubDate>
        <category>Data Analysis</category>
        <dc:creator>Martin_Pyka</dc:creator>
        <guid isPermaLink="false">141@/discussions</guid>
        <description><![CDATA[Hello,

I am working on a 3d computational model of the rat hippocampus and entorhinal cortex, using Parametric Anatomical Modeling:

http://journal.frontiersin.org/Journal/10.3389/fnana.2014.00091/abstract

Here is a demonstration of the technique and the model on Youtube:
https://www.youtube.com/watch?v=W-BrAcMUiYI

Watching the videos about the Clarity method, I noted that these volumetric data really help to understand how the projections in space look like. This is something, which is not visible in the standard data like the Allen Brain Atlas.

I was wondering whether anybody would be willing to share some raw volumetric data of the hippocampus of the mouse or rat with us. In particular, we would be interested in understanding, how the projections from entorhinal cortex to the hippocampus and back look like in space. But also the volumetric data about the hippocampal formation itself would be of great help to make our model (we are focusing right now on the primary excitatory connections) as realistic as possible.

You can also contact me via email: m.pyka@rub.de

Best,
Martin Pyka 

-- 
Dr. Martin Pyka
Ruhr-University Bochum
Mercator Research Group "Structure of Memory"
Faculty of Psychology
Germany
Email: m.pyka@rub.de
Web:
http://www.martinpyka.de
http://cns.mrg1.rub.de/index.php/people/128-martin-pyka]]>
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