SpikeGLX 20231207

Sgl_help/Metadata_30.html

@@ -285,7 +285,7 @@ <h2 id="imec">Imec</h2>
 <p>This is the probe serial number.</p>
 <pre><code>imDatPrb_type=21</code></pre>
 <p>This is the probe type {0=NP1.0, 21=NP2.0(1-shank), 24=NP2.0(4-shank)}.</p>
-<pre><code>imErrFlags_IS_CT_SR_LK_PP_SY=0 0 0 0 0 0</code></pre>
+<pre><code>imErrFlags0_IS_CT_SR_LK_PP_SY=0 0 0 0 0 0</code></pre>
 <p>For each imec stream we monitor the cumulative count of several error flags. These are labeled {COUNT, SERDES, LOCK, POP, SYNC}. The metadata field 'IS' = 1 if any error occurred, 0 otherwise. I.e., &quot;is an error.&quot;</p>
 <p>Any instances of these errors implies that samples have been dropped. It is not possible to tell how many samples are dropped from these counts. All you can tell is that some of the data being transmitted from the device are corrupt or missing.</p>
 <p>These flags correspond to bits of the status/SYNC word that is visible as the last channel in the graphs and in your recorded data:</p>

firmware/index.html

@@ -159,7 +159,7 @@ <h2 id="fix-imec-module-doesnt-work-in-my-chassis">FIX: Imec Module Doesn't Work
 designed the module firmware for X4 and higher slots.</p>
 <p>Modules have two copies of the firmware. The normal/working copy is loaded,
 unless you power-up with the ISP button depressed, in which case the boot
-image is loaded. Note the the boot image is a backup copy in case the working
+image is loaded. Note the boot image is a backup copy in case the working
 copy is corrupted.</p>
 <p>In roughly Q2 2022, imec began shipping modules with an X1-compatible
 working image, but not an X1-compatible golden image. By Q2 2023, both

help/NIDriverInstall/NI_driver_installation/index.html

@@ -163,7 +163,7 @@ <h1 id="ni-chassis-and-io-card-setup">NI chassis and I/O card setup</h1>
 <hr />
 <p>This document covers the steps to install the necessary software for an NI
 chassis, NI remote control module, and an NI acquisition device for
-non-neural signals. We've selected a PXI-6133 module in these example.</p>
+non-neural signals. We've selected a PXI-6133 module in these examples.</p>
 <blockquote>
 <p>SpikeGLX will work with multifunction IO S-series 61XX, M-series 62XX,
 X-series 63XX devices, and with digital-only 653X devices. Moreover, you

help/catgt_tshift/catgt_tshift/index.html

@@ -140,11 +140,11 @@
               <ul class="nav flex-column">
               </ul>
             </li>
-            <li class="nav-item" data-level="2"><a href="#what-happened-to-global-demux" class="nav-link">What Happened to Global Demux?</a>
+            <li class="nav-item" data-level="2"><a href="#what-is-global-demux-gbldmx" class="nav-link">What is global demux (gbldmx)?</a>
               <ul class="nav flex-column">
               </ul>
             </li>
-            <li class="nav-item" data-level="2"><a href="#what-about-catgt-loccar" class="nav-link">What about CatGT loccar?</a>
+            <li class="nav-item" data-level="2"><a href="#what-is-local-car-loccar" class="nav-link">What is local CAR (loccar)?</a>
               <ul class="nav flex-column">
               </ul>
             </li>
@@ -189,7 +189,7 @@ <h2 id="artifact-corrections-car-gfix">Artifact Corrections {CAR, Gfix}</h2>
 channels and that haven't saturated on any channels.</p>
 <p><strong>Zeroing (CatGT -gfix option)</strong></p>
 <p>Sometimes the hardware experiences a large electrical insult that affects
-all channels in a nonunifom way. This may arise from licking, chewing,
+all channels in a nonuniform way. This may arise from licking, chewing,
 head banging or laser stimulation events. In these cases CAR won't
 work as well. CatGT can detect these events and replace them with zeros.</p>
 <p>This option is specified, for example, as follows: <code>-gfix=0.40,0.10,0.02</code>.
@@ -215,17 +215,42 @@ <h2 id="artifact-corrections-car-gfix">Artifact Corrections {CAR, Gfix}</h2>
 <li>Right: -gblcar -gfix; All artifacts removed.</li>
 </ul>
 <p><img alt="&lt;BR/&gt;" src="../car.jpg" /></p>
-<h2 id="what-happened-to-global-demux">What Happened to Global Demux?</h2>
-<p>Before version 2.2, and before tshift was implemented, CatGT offered a
--gbldmx option. This separated the channels into groups that are sampled
-concurrently so suffer no time shifts within the group. CAR was performed
-on a group by group basis which often outperformed CAR on all channels.
-Because the number of channels in a multiplex group was small the averages
-were noisier than we can achieve by tshifting all channels into one large
+<h2 id="what-is-global-demux-gbldmx">What is global demux (gbldmx)?</h2>
+<p>The CatGT gbldmx option separates the channels into groups that are sampled
+concurrently so suffer no time shifts within the group. CAR is then performed
+on a group by group basis which has advantages and disadvantages compared to
+doing (tshift + gblcar).</p>
+<p>Disadvantages:</p>
+<ul>
+<li>
+<p>Because the number of channels in a multiplex group is small the averages
+are noisier than we can achieve by tshifting all channels into one large
 group and applying CAR after that.</p>
-<p>Moreover, tshifting the data improves the results of other downstream
-operations like whitening and average waveform spread.</p>
-<h2 id="what-about-catgt-loccar">What about CatGT loccar?</h2>
+</li>
+<li>
+<p>Outlier channels have a stronger biasing effect with smaller sample sizes.</p>
+</li>
+<li>
+<p>The correction factors tend to be larger (small channel count in denominator)
+than with CAR, and that can produce overcorrection artifacts that look like
+spikes (often small inverted spikes).</p>
+</li>
+</ul>
+<p>When to use gbldmx:</p>
+<ul>
+<li>
+<p>The probe sampling rate is 30 kHz, so noise faster than 15 kHz is not
+adequately sampled, and therefore, not accurately propagated to other
+channel groups by the tshift operation. So for very fast noise artifacts,
+gbldmx may produce better cancellation within each subsampling group.</p>
+</li>
+<li>
+<p>gbldmx usually outperforms gblcar when tshift is omitted. You may want
+to omit tshift in CatGT, using the -no_tshift option, if tshift will be
+applied by some later component in your analysis pipeline.</p>
+</li>
+</ul>
+<h2 id="what-is-local-car-loccar">What is local CAR (loccar)?</h2>
 <p>CatGT offers the option to do local CAR over a ring of channels. The idea
 is that for each channel a disk is used to average the signal of neighbor
 channels, but an inner disk (containing a potential spike footprint) is
@@ -253,7 +278,7 @@ <h2 id="what-about-catgt-loccar">What about CatGT loccar?</h2>
 </ul>
 <h2 id="what-about-lfp">What about LFP?</h2>
 <p>Tshift is valuable for aligning LFP channels. CAR is not recommended when
-analyzing low freqencies: LFP varies slowly over the whole shank, making
+analyzing low frequencies: LFP varies slowly over the whole shank, making
 distant channels a bad reference for correcting noise.</p>
 <p><em>fin</em></p></div>
             </div>

help/syncEdges/Sync_edges/index.html

@@ -566,7 +566,7 @@ <h4 id="extractors-inverted-pulse">Extractors inverted pulse</h4>
 <h4 id="extractors-bf-bit-field">Extractors bf (bit-field)</h4>
 <p>The -xd and -xid options treat each bit of a digital word as an individual
 line. In contrast, the -bf option interprets a contiguous group of bits
-as a non-negative n-bit binary number. The -bf extactor reports value
+as a non-negative n-bit binary number. The -bf extractor reports value
 transitions: the newest value and the time it changed, in two separate files.
 Following <strong>-xa=js,ip,word</strong>, the parameters are:</p>
 <ul>

index.html

@@ -265,7 +265,7 @@ <h2 id="latest-application-downloads">Latest Application Downloads</h2>
 firmware versions.</p>
 </blockquote>
 <ul>
-<li><a href="App/Release_v20230905-phase30.zip">Release 20230905-phase30</a>...<a href="Readme/Readme_v20230905-phase30.txt">Readme</a> : Spike Viewer, bug fixes, imec v3.62</li>
+<li><a href="App/Release_v20231207-phase30.zip">Release 20231207-phase30</a>...<a href="Readme/Readme_v20231207-phase30.txt">Readme</a> : NP1016, imec v3.62.1</li>
 </ul>
 <p><strong>Xilinx Kintex versions not covered by 3.0</strong>:</p>
 <ul>
@@ -278,9 +278,9 @@ <h2 id="latest-application-downloads">Latest Application Downloads</h2>
 versions there as long as you run one at a time:</p>
 </blockquote>
 <pre><code>SpikeGLX\
-    Release_v20230905-phase30.zip
+    Release_v20231207-phase30.zip
     Release_v20200520-phase3B2.zip
-    Release_v20230905-phase30\
+    Release_v20231207-phase30\
     Release_v20200520-phase3B2\
     Drivers\
         Enclustra_Windows_10&amp;11\
@@ -592,5 +592,5 @@ <h4 class="modal-title" id="keyboardModalLabel">Keyboard Shortcuts</h4>
 
 <!--
 MkDocs version : 1.1.2
-Build Date UTC : 2023-12-18 19:07:47.654976+00:00
+Build Date UTC : 2024-01-30 02:38:16.586664+00:00
 -->

legacy/index.html

@@ -201,6 +201,7 @@ <h2 id="imec-project-phases">Imec Project Phases</h2>
 <h2 id="older-versions">Older Versions</h2>
 <p><strong>30</strong>:</p>
 <ul>
+<li><a href="../App/Release_v20230905-phase30.zip">Release 20230905-phase30</a>...<a href="../Readme/Readme_v20230905-phase30.txt">Readme</a> : Spike Viewer, bug fixes, imec v3.62</li>
 <li><a href="../App/Release_v20230815-phase30.zip">Release 20230815-phase30</a>...<a href="../Readme/Readme_v20230815-phase30.txt">Readme</a> : NP2014, low latency mode, imec v3.62</li>
 <li><a href="../App/Release_v20230425-phase30.zip">Release 20230425-phase30</a>...<a href="../Readme/Readme_v20230425-phase30.txt">Readme</a> : Anatomy data, better SNR, imec v3.60</li>
 <li><a href="../App/Release_v20230411-phase30.zip">Release 20230411-phase30</a>...<a href="../Readme/Readme_v20230411-phase30.txt">Readme</a> : 2.0 probes, Fix PH2B headstage, imec v3.60</li>

new/index.html

@@ -140,6 +140,10 @@
                     <div class="col-md-9" role="main">
 
 <h1 id="whats-new-on-the-site">What's New On The Site?</h1>
+<p>January 29, 2024</p>
+<ul>
+<li>SpikeGLX 20231207-phase30 (NP1016, imec 3.62.1).</li>
+</ul>
 <p>December 18, 2023</p>
 <ul>
 <li>CatGT 4.3 (Supercat can join runs with varied sample rates).</li>

sglhome/docs/Help/NIDriverInstall/NI_driver_installation.md

@@ -4,7 +4,7 @@
 
 This document covers the steps to install the necessary software for an NI
 chassis, NI remote control module, and an NI acquisition device for
-non-neural signals. We've selected a PXI-6133 module in these example.
+non-neural signals. We've selected a PXI-6133 module in these examples.
 
 >SpikeGLX will work with multifunction IO S-series 61XX, M-series 62XX,
 X-series 63XX devices, and with digital-only 653X devices. Moreover, you

sglhome/docs/Help/SyncEdges/Sync_edges.md

@@ -375,7 +375,7 @@ level and deflect toward lower values.
 
 The -xd and -xid options treat each bit of a digital word as an individual
 line. In contrast, the -bf option interprets a contiguous group of bits
-as a non-negative n-bit binary number. The -bf extactor reports value
+as a non-negative n-bit binary number. The -bf extractor reports value
 transitions: the newest value and the time it changed, in two separate files.
 Following **-xa=js,ip,word**, the parameters are:
 

sglhome/docs/firmware.md

@@ -14,7 +14,7 @@ designed the module firmware for X4 and higher slots.
 
 Modules have two copies of the firmware. The normal/working copy is loaded,
 unless you power-up with the ISP button depressed, in which case the boot
-image is loaded. Note the the boot image is a backup copy in case the working
+image is loaded. Note the boot image is a backup copy in case the working
 copy is corrupted.
 
 In roughly Q2 2022, imec began shipping modules with an X1-compatible

sglhome/docs/help/catgt_tshift/catgt_tshift.md

@@ -38,7 +38,7 @@ channels and that haven't saturated on any channels.
 **Zeroing (CatGT -gfix option)**
 
 Sometimes the hardware experiences a large electrical insult that affects
-all channels in a nonunifom way. This may arise from licking, chewing,
+all channels in a nonuniform way. This may arise from licking, chewing,
 head banging or laser stimulation events. In these cases CAR won't
 work as well. CatGT can detect these events and replace them with zeros.
 
@@ -69,20 +69,37 @@ Figure panels (from SpikeGLX FileViewer):
 
 ![<BR/>](car.jpg)
 
-## What Happened to Global Demux?
+## What is global demux (gbldmx)?
 
-Before version 2.2, and before tshift was implemented, CatGT offered a
--gbldmx option. This separated the channels into groups that are sampled
-concurrently so suffer no time shifts within the group. CAR was performed
-on a group by group basis which often outperformed CAR on all channels.
-Because the number of channels in a multiplex group was small the averages
-were noisier than we can achieve by tshifting all channels into one large
+The CatGT gbldmx option separates the channels into groups that are sampled
+concurrently so suffer no time shifts within the group. CAR is then performed
+on a group by group basis which has advantages and disadvantages compared to
+doing (tshift + gblcar).
+
+Disadvantages:
+
+- Because the number of channels in a multiplex group is small the averages
+are noisier than we can achieve by tshifting all channels into one large
 group and applying CAR after that.
 
-Moreover, tshifting the data improves the results of other downstream
-operations like whitening and average waveform spread.
+- Outlier channels have a stronger biasing effect with smaller sample sizes.
+
+- The correction factors tend to be larger (small channel count in denominator)
+than with CAR, and that can produce overcorrection artifacts that look like
+spikes (often small inverted spikes).
+
+When to use gbldmx:
+
+- The probe sampling rate is 30 kHz, so noise faster than 15 kHz is not
+adequately sampled, and therefore, not accurately propagated to other
+channel groups by the tshift operation. So for very fast noise artifacts,
+gbldmx may produce better cancellation within each subsampling group.
+
+- gbldmx usually outperforms gblcar when tshift is omitted. You may want
+to omit tshift in CatGT, using the -no_tshift option, if tshift will be
+applied by some later component in your analysis pipeline.
 
-## What about CatGT loccar?
+## What is local CAR (loccar)?
 
 CatGT offers the option to do local CAR over a ring of channels. The idea
 is that for each channel a disk is used to average the signal of neighbor
@@ -110,7 +127,7 @@ setting a fairly large outer radius to balance locality vs smoothness.
 ## What about LFP?
 
 Tshift is valuable for aligning LFP channels. CAR is not recommended when
-analyzing low freqencies: LFP varies slowly over the whole shank, making
+analyzing low frequencies: LFP varies slowly over the whole shank, making
 distant channels a bad reference for correcting noise.
 
 

sglhome/docs/index.md

@@ -64,7 +64,7 @@ Latest release highlights:
 >Important: Please read the `README` file for instructions regarding imec
 firmware versions.
 
-* [Release 20230905-phase30](App/Release_v20230905-phase30.zip)...[Readme](Readme/Readme_v20230905-phase30.txt) : Spike Viewer, bug fixes, imec v3.62
+* [Release 20231207-phase30](App/Release_v20231207-phase30.zip)...[Readme](Readme/Readme_v20231207-phase30.txt) : NP1016, imec v3.62.1
 
 **Xilinx Kintex versions not covered by 3.0**:
 
@@ -77,9 +77,9 @@ versions there as long as you run one at a time:
 
 ```
 SpikeGLX\
-    Release_v20230905-phase30.zip
+    Release_v20231207-phase30.zip
     Release_v20200520-phase3B2.zip
-    Release_v20230905-phase30\
+    Release_v20231207-phase30\
     Release_v20200520-phase3B2\
     Drivers\
         Enclustra_Windows_10&11\

sglhome/docs/legacy.md

@@ -48,6 +48,7 @@ can be used after updating their firmware, which can be done via SpikeGLX.
 
 **30**:
 
+* [Release 20230905-phase30](../App/Release_v20230905-phase30.zip)...[Readme](../Readme/Readme_v20230905-phase30.txt) : Spike Viewer, bug fixes, imec v3.62
 * [Release 20230815-phase30](../App/Release_v20230815-phase30.zip)...[Readme](../Readme/Readme_v20230815-phase30.txt) : NP2014, low latency mode, imec v3.62
 * [Release 20230425-phase30](../App/Release_v20230425-phase30.zip)...[Readme](../Readme/Readme_v20230425-phase30.txt) : Anatomy data, better SNR, imec v3.60
 * [Release 20230411-phase30](../App/Release_v20230411-phase30.zip)...[Readme](../Readme/Readme_v20230411-phase30.txt) : 2.0 probes, Fix PH2B headstage, imec v3.60

sglhome/docs/new.md

@@ -1,5 +1,9 @@
 # What's New On The Site?
 
+January 29, 2024
+
+* SpikeGLX 20231207-phase30 (NP1016, imec 3.62.1).
+
 December 18, 2023
 
 * CatGT 4.3 (Supercat can join runs with varied sample rates).

sitemap.xml

@@ -1,43 +1,43 @@
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