diff --git a/tools/hicexplorer/chicSignificantInteractions.xml b/tools/hicexplorer/chicSignificantInteractions.xml
index f4a835fed11..8110d179211 100644
--- a/tools/hicexplorer/chicSignificantInteractions.xml
+++ b/tools/hicexplorer/chicSignificantInteractions.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>computes viewpoints with the given reference points and a background model</description>
     <macros>
         <token name="@BINARY@">chicSignificantInteractions</token>
diff --git a/tools/hicexplorer/chicViewpoint.xml b/tools/hicexplorer/chicViewpoint.xml
index 80a6288823e..7e4a81cdfb6 100644
--- a/tools/hicexplorer/chicViewpoint.xml
+++ b/tools/hicexplorer/chicViewpoint.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>computes viewpoints with the given reference points and a background model.</description>
     <macros>
         <token name="@BINARY@">chicViewpoint</token>
diff --git a/tools/hicexplorer/chicViewpointBackgroundModel.xml b/tools/hicexplorer/chicViewpointBackgroundModel.xml
index ac2692aaca4..85bf6caea4e 100644
--- a/tools/hicexplorer/chicViewpointBackgroundModel.xml
+++ b/tools/hicexplorer/chicViewpointBackgroundModel.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>compute a background model for cHi-C / HiChIP data</description>
     <macros>
         <token name="@BINARY@">chicViewpointBackgroundModel</token>
diff --git a/tools/hicexplorer/hicAdjustMatrix.xml b/tools/hicexplorer/hicAdjustMatrix.xml
index b1beee8178c..223f37d6e72 100644
--- a/tools/hicexplorer/hicAdjustMatrix.xml
+++ b/tools/hicexplorer/hicAdjustMatrix.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>adjust the shape of a Hi-C matrix</description>
     <macros>
         <token name="@BINARY@">hicAdjustMatrix</token>
diff --git a/tools/hicexplorer/hicAggregateContacts.xml b/tools/hicexplorer/hicAggregateContacts.xml
index 51ee3de365e..a91ad72d457 100644
--- a/tools/hicexplorer/hicAggregateContacts.xml
+++ b/tools/hicexplorer/hicAggregateContacts.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>allow plotting of aggregated Hi-C contacts between regions specified in a file</description>
     <macros>
         <token name="@BINARY@">hicAggregateContacts</token>
diff --git a/tools/hicexplorer/hicAverageRegions.xml b/tools/hicexplorer/hicAverageRegions.xml
index f4d1bb13d3a..474c32f836f 100644
--- a/tools/hicexplorer/hicAverageRegions.xml
+++ b/tools/hicexplorer/hicAverageRegions.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicaverageregions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>sums Hi-C contacts around given reference points and computes their average.</description>
     <macros>
         <token name="@BINARY@">hicAverageRegions</token>
diff --git a/tools/hicexplorer/hicBuildMatrix.xml b/tools/hicexplorer/hicBuildMatrix.xml
index c9d3dbcefb1..4e967a6afb7 100644
--- a/tools/hicexplorer/hicBuildMatrix.xml
+++ b/tools/hicexplorer/hicBuildMatrix.xml
@@ -1,12 +1,10 @@
-<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>create a contact matrix</description>
     <macros>
         <token name="@BINARY@">hicBuildMatrix</token>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.19">samtools</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 
         mkdir ./QCfolder &&
diff --git a/tools/hicexplorer/hicBuildMatrixMicroC.xml b/tools/hicexplorer/hicBuildMatrixMicroC.xml
new file mode 100644
index 00000000000..1ecb70aec64
--- /dev/null
+++ b/tools/hicexplorer/hicBuildMatrixMicroC.xml
@@ -0,0 +1,223 @@
+<tool id="hicexplorer_hicbuildmatrixmicroc" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>create a contact matrix</description>
+    <macros>
+        <token name="@BINARY@">hicBuildMatrixMicroC</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+
+        mkdir ./QCfolder &&
+        mkdir '$qc.files_path' &&
+        @BINARY@
+            --samFiles
+            #for $repeat in $samFiles:
+                '${repeat.samFile}'
+            #end for
+
+            #if $maxLibraryInsertSize:
+                --maxLibraryInsertSize $maxLibraryInsertSize
+            #end if
+
+            #if $binSizes:
+                --binSize
+                #for $repeat in $binSizes
+                    '${repeat.binSize}'
+                #end for
+            #end if
+
+            #if $chromosomeSizes:
+                --chromosomeSizes '$chromosomeSizes'
+            #end if
+            #if $dbKey:
+                --genomeAssembly '$dbKey'
+            #else
+                --genomeAssembly '$samFiles[0].samFile.metadata.dbkey'
+            #end if
+
+            #if $region:
+                --region '$region'
+            #end if
+
+            --outFileName 'matrix.$outputFormat'
+
+            #if $outBam:
+                $outBam ./unsorted.bam
+            #end if
+
+            $keepSelfCircles
+            $skipDuplicationCheck
+
+            #if $minMappingQuality and $minMappingQuality is not None:
+                --minMappingQuality $minMappingQuality
+            #end if
+
+            --threads @THREADS@
+
+            --QCfolder ./QCfolder
+        &&
+        mv ./QCfolder/* $qc.files_path/
+        &&
+        mv '$qc.files_path/hicQC.html' '$qc'
+        && mv "$qc.files_path"/*.log raw_qc
+        && mv matrix.$outputFormat matrix
+        #if $outBam:
+            && samtools sort -@ @THREADS@ -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
+        #end if
+]]>
+    </command>
+    <inputs>
+        <!-- can we use multiple=True here with min="2" and max="2" ? -->
+        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
+            <param name="samFile" type="data" format="sam,qname_input_sorted.bam">
+            </param>
+        </repeat>
+
+        <param argument="--maxLibraryInsertSize" type="integer" optional="true" value="" label="Maximum library insert size defines different cut offs based on the maximum expected library size" help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
+                        which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates
+                        belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
+                        is too far away from the nearest restriction site." />
+
+        <repeat name="binSizes" title="Bin size in bp" min="1" help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
+                Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file.">
+            <param argument="--binSize" type="integer" optional="true" value="" label="Bin size in bp" />
+        </repeat>
+
+        <expand macro="region" />
+        <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." />
+        <expand macro="minMappingQuality" />
+        <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." />
+        <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected
+                    Usually the sizes can be determined from the SAM/BAM input files, however,
+                    for cHi-C or scHi-C it can be that at the start or end no data is present.
+                    Please consider that this option causes that only reads are considered which are on the listed chromosomes.
+                    Use this option to guarantee fixed sizes. An example file is available via UCSC:
+                    http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" />
+        <param name="dbKey" type="text" optional="true" label="Use this dbkey for your history genome"
+        help="You can set the reference genome in your history as metadata. In case you have not you can specify it here." />
+
+        <param argument="--outBam" type="boolean" truevalue="--outBam" falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam
+                    file containing all valid Hi-C reads can be created
+                    using this option. This bam file could be useful to
+                    inspect the distribution of valid Hi-C reads pairs or
+                    for other downstream analyses, but is not used by any
+                    HiCExplorer tool. Computation will be significantly
+                    longer if this option is set." />
+
+        <param name="outputFormat" type="select" label="Output file format">
+            <option value="h5">HiCExplorer format</option>
+            <option value="cool">cool</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="outfileBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}">
+            <filter>outBam</filter>
+        </data>
+        <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
+            <change_format>
+                <when input="outputFormat" value="cool" format="cool" />
+            </change_format>
+        </data>
+        <data name="qc" format="html" label="${tool.name} QC on ${on_string}" />
+        <data name="raw_qc" from_work_dir="raw_qc" format="txt" label="${tool.name} raw QC on ${on_string}" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="4">
+            <repeat name="samFiles">
+                <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
+            </repeat>
+            <repeat name="samFiles">
+                <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
+            </repeat>
+            <param name="outputFormat" value="h5" />
+            <repeat name="binSizes">
+                <param name="binSize" value="5000" />
+            </repeat>
+            <param name="outBam" value="True" />
+            <output name="outfileBam" file="small_test_matrix_result_sorted_microc.bam" compare="diff" lines_diff="2" ftype="bam" />
+            <output name="outFileName" ftype="h5">
+                <assert_contents>
+                    <has_h5_keys keys="intervals,matrix" />
+                </assert_contents>
+            </output>
+            <output name="raw_qc" file="raw_qc_report_micro-c" compare="diff" lines_diff="2" />
+        </test>
+        <test expect_num_outputs="4">
+            <repeat name="samFiles">
+                <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
+            </repeat>
+            <repeat name="samFiles">
+                <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
+            </repeat>
+            <repeat name="binSizes">
+                <param name="binSize" value="5000" />
+            </repeat>
+            <param name="outputFormat" value="cool" />
+            <param name="outBam" value="True" />
+            <output name="outfileBam" file="small_test_matrix_result_sorted_microc.bam" compare="diff" lines_diff="2" ftype="bam" />
+            <output name="outFileName" ftype="cool">
+                <assert_contents>
+                    <has_h5_keys keys="bins,chroms,indexes,pixels" />
+                </assert_contents>
+            </output>
+            <output name="raw_qc" file="raw_qc_report_micro-c" compare="diff" lines_diff="2" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Creation of the contact matrix
+===============================
+
+
+**hicBuildMatrixMicroC** generates a contact matrix from Micro-C read pairs, using paired-end Hi-C reads mapped to a reference genome. This process requires two SAM or BAM files: one for the first mate and one for the second mate of the paired-end reads. These files must be unaligned by position (i.e., not sorted). Unlike traditional Hi-C data, where restriction enzyme cut sites determine resolution, Micro-C does not rely on such sites. Instead, the contact matrix is created using a fixed bin size (e.g., 10,000 bp). 
+
+Additionally, **hicBuildMatrixMicroC** produces a quality control report to evaluate the quality of the Hi-C reads, aiding in determining the success of both the experimental protocol and sequencing process.
+
+
+_________________
+
+
+Usage
+-----
+
+
+This tool is designed to work with paired SAM/BAM files generated by alignment software supporting local alignment, such as Bowtie2, using the `--local` alignment option for paired-end reads. Both files should represent properly mapped reads.
+
+_________________
+
+
+Output
+------
+
+**hicBuildMatrixMicroC** generates the following outputs:
+
+- **Contact Matrix**: A matrix compatible with HiCExplorer for downstream analyses.
+- **Accepted Alignments BAM File**: This file includes valid Hi-C read pairs. While not directly used by HiCExplorer, it is valuable for inspecting the distribution of valid reads, such as around restriction enzyme sites, or for other analyses.
+- **Quality Control Report**: This report provides an evaluation of the Hi-C data, helping to determine whether the library preparation and experimental workflow were successful.
+
+
+Example plot
+++++++++++++
+
+.. image:: hicPlotMatrix.png
+   :width: 50%
+
+*Contact matrix of *Drosophila melanogaster* embryos built using **hicBuildMatrix**. The example shows Micro-C data, visualized with `hicPlotMatrix`. Bins were merged to a 25 kb resolution using `hicMergeMatrixBins` before plotting.*
+
+
+
+
+Quality report
+++++++++++++++
+
+A detailed quality control report accompanies the contact matrix. This report is similar to the one generated by **hicBuildMatrix**, but excludes information specific to restriction cut sites, such as dangling ends and self-circles, as these features are not applicable to Micro-C data.
+
+
+_________________
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_.
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]>    </help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/hicexplorer/macros.xml b/tools/hicexplorer/macros.xml
index 5e0c5e5230b..d161e2a1c09 100644
--- a/tools/hicexplorer/macros.xml
+++ b/tools/hicexplorer/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@TOOL_VERSION@">3.7.5</token>
+    <token name="@TOOL_VERSION@">3.7.6</token>
     <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">23.0</token>
     <token name="@USE_RANGE@">
diff --git a/tools/hicexplorer/test-data/cHi-C/chicExportData/aggregate.tar.gz b/tools/hicexplorer/test-data/cHi-C/chicExportData/aggregate.tar.gz
index ff0e9e73a29..ce625589952 100644
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diff --git a/tools/hicexplorer/test-data/cHi-C/chicQualityControl/histogram.png b/tools/hicexplorer/test-data/cHi-C/chicQualityControl/histogram.png
index 832ff04c8ba..5cd3a5acd65 100644
Binary files a/tools/hicexplorer/test-data/cHi-C/chicQualityControl/histogram.png and b/tools/hicexplorer/test-data/cHi-C/chicQualityControl/histogram.png differ
diff --git a/tools/hicexplorer/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter b/tools/hicexplorer/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
index 7f07c5a31bd..3a614d0e461 100644
--- a/tools/hicexplorer/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
+++ b/tools/hicexplorer/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.7.5
+# Created with chicQualityControl version 3.7.6
 # A sparsity of -1.0 indicates a faulty reference point e.g. no data for this reference point was in the matrix.
 # Used Matrices 0_matrix.cool	1_matrix.cool	
 # Chromosome	Start	End	Sparsity 0_matrix.cool	Sparsity 1_matrix.cool
diff --git a/tools/hicexplorer/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report b/tools/hicexplorer/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report
index 5c76f7db3b8..123c7c5c746 100644
--- a/tools/hicexplorer/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report
+++ b/tools/hicexplorer/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report
@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.7.5
+# Created with chicQualityControl version 3.7.6
 # QC report for matrices: 0_matrix.cool 1_matrix.cool 
 #Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
 
diff --git a/tools/hicexplorer/test-data/cHi-C/chicQualityControl/sparsity.png b/tools/hicexplorer/test-data/cHi-C/chicQualityControl/sparsity.png
index 6e458c207cb..cad966d820b 100644
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diff --git a/tools/hicexplorer/test-data/cHi-C/plots.tar.gz b/tools/hicexplorer/test-data/cHi-C/plots.tar.gz
index b62da2cdf71..b7c6c3a1fc9 100644
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diff --git a/tools/hicexplorer/test-data/hicAggregateContacts_results1.png b/tools/hicexplorer/test-data/hicAggregateContacts_results1.png
index c48a387c71f..2897406dec0 100644
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diff --git a/tools/hicexplorer/test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png b/tools/hicexplorer/test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png
index e1b61d36d2a..1d26429844e 100644
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diff --git a/tools/hicexplorer/test-data/hicCompartmentsPolarization/output_matrix.npz b/tools/hicexplorer/test-data/hicCompartmentsPolarization/output_matrix.npz
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diff --git a/tools/hicexplorer/test-data/hicConvertFormat/small_test_matrix_chr4.homer b/tools/hicexplorer/test-data/hicConvertFormat/small_test_matrix_chr4.homer
index d46dbe649e5..47d37f4f727 100644
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diff --git a/tools/hicexplorer/test-data/hicCorrectMatrix/diagnostic_plot.png b/tools/hicexplorer/test-data/hicCorrectMatrix/diagnostic_plot.png
index d7b50989830..d483c13cff9 100644
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diff --git a/tools/hicexplorer/test-data/hicCorrelate_heatmap_result1.png b/tools/hicexplorer/test-data/hicCorrelate_heatmap_result1.png
index 45c0b657502..3d0ded293b2 100644
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diff --git a/tools/hicexplorer/test-data/hicCorrelate_scatter_result1.png b/tools/hicexplorer/test-data/hicCorrelate_scatter_result1.png
index d1b6ce38b37..88d4d308e97 100644
Binary files a/tools/hicexplorer/test-data/hicCorrelate_scatter_result1.png and b/tools/hicexplorer/test-data/hicCorrelate_scatter_result1.png differ
diff --git a/tools/hicexplorer/test-data/hicDetectLoops/loops.bedgraph b/tools/hicexplorer/test-data/hicDetectLoops/loops.bedgraph
index e69de29bb2d..1a567c347c8 100644
--- a/tools/hicexplorer/test-data/hicDetectLoops/loops.bedgraph
+++ b/tools/hicexplorer/test-data/hicDetectLoops/loops.bedgraph
@@ -0,0 +1,2 @@
+chr3L	640000	645000	chr3L	645000	650000	0.10258046718611576
+chr2L	18670000	18675000	chr2L	18675000	18680000	0.23000508888575644
diff --git a/tools/hicexplorer/test-data/hicDifferentialTAD/accepted.txt b/tools/hicexplorer/test-data/hicDifferentialTAD/accepted.txt
index 28f942bbe41..1be256bb9f9 100644
--- a/tools/hicexplorer/test-data/hicDifferentialTAD/accepted.txt
+++ b/tools/hicexplorer/test-data/hicDifferentialTAD/accepted.txt
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicDifferentialTAD version 3.7.5
+# Created with HiCExplorer's hicDifferentialTAD version 3.7.6
 # H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential.
 # Accepted regions with Wilcoxon rank-sum test to p-value: 1.0  with used mode: all and modeReject: one 
 # Chromosome	start	end	name	score	strand	p-value left-inter-TAD	p-value right-inter-TAD	p-value intra-TAD	W left-inter-TAD	W right-inter-TAD	W intra-TAD
diff --git a/tools/hicexplorer/test-data/hicDifferentialTAD/rejected.txt b/tools/hicexplorer/test-data/hicDifferentialTAD/rejected.txt
index 726cfac00ae..e99ddf464a3 100644
--- a/tools/hicexplorer/test-data/hicDifferentialTAD/rejected.txt
+++ b/tools/hicexplorer/test-data/hicDifferentialTAD/rejected.txt
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicDifferentialTAD version 3.7.5
+# Created with HiCExplorer's hicDifferentialTAD version 3.7.6
 # H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential.
 # Rejected regions with Wilcoxon rank-sum test to p-value: 1.0  with used mode: all and modeReject: one 
 # Chromosome	start	end	name	score	strand	p-value left-inter-TAD	p-value right-inter-TAD	p-value intra-TAD	W left-inter-TAD	W right-inter-TAD	W intra-TAD
diff --git a/tools/hicexplorer/test-data/hicHyperoptDetectLoops/loops.bedgraph b/tools/hicexplorer/test-data/hicHyperoptDetectLoops/loops.bedgraph
index b56bafb3e8f..f3df687a188 100644
--- a/tools/hicexplorer/test-data/hicHyperoptDetectLoops/loops.bedgraph
+++ b/tools/hicexplorer/test-data/hicHyperoptDetectLoops/loops.bedgraph
@@ -1,3 +1,3 @@
-# Created by HiCExplorer hicHyperoptDetectLoops 3.7.3
+# Created by HiCExplorer hicHyperoptDetectLoops 3.7.6
 
-{'chrPrefixLoops': None, 'matrixFile': 'matrix.cool', 'maxLoopDistance': 2300000, 'maximumNumberOfLoops': 5, 'oet': 1.230889168935347, 'p': 0.048940366161874596, 'peakWidth': 6, 'pit': 22.88867979095296, 'pp': 0.13365961880597724, 'proteinFile': '/tmp/tmpjkr0wi60/files/6/a/7/dataset_6a78c4eb-7f74-459b-9ed8-08972cc0c5f4.dat', 'resolution': 2, 'threads': 1, 'windowSize': 6}
\ No newline at end of file
+{'chrPrefixLoops': None, 'matrixFile': 'matrix.cool', 'maxLoopDistance': 1300000, 'maximumNumberOfLoops': 5, 'oet': 2.8714859798937415, 'p': 0.012586549394837264, 'peakWidth': 8, 'pit': 63.88073951584609, 'pp': 0.06112040451977812, 'proteinFile': '/tmp/tmpgf9pvov_/files/2/9/7/dataset_2978768e-39c0-4648-aa6e-8f81c54806cb.dat', 'resolution': 2, 'threads': 1, 'windowSize': 11}
\ No newline at end of file
diff --git a/tools/hicexplorer/test-data/hicInfo/hicInfo_output.txt b/tools/hicexplorer/test-data/hicInfo/hicInfo_output.txt
index a721b369c10..c7a78a3bb01 100644
--- a/tools/hicexplorer/test-data/hicInfo/hicInfo_output.txt
+++ b/tools/hicexplorer/test-data/hicInfo/hicInfo_output.txt
@@ -1,4 +1,4 @@
-# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.5
+# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.6
 File:	matrix_name.h5
 Size:	33,754
 Bin_length:	5000
diff --git a/tools/hicexplorer/test-data/hicInterIntraTAD/output.txt b/tools/hicexplorer/test-data/hicInterIntraTAD/output.txt
index 699f4075cd6..1e412b38828 100644
--- a/tools/hicexplorer/test-data/hicInterIntraTAD/output.txt
+++ b/tools/hicexplorer/test-data/hicInterIntraTAD/output.txt
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicInterIntraTAD version 3.7.5
+# Created with HiCExplorer's hicInterIntraTAD version 3.7.6
 # Chromosome	start	end	name	score	strand	inter_left_sum	inter_right_sum	inter_left_density	inter_right_density	inter_left_number_of_contacts	inter_right_number_of_contacts	inter_left_number_of_contacts_nnz	inter_right_number_of_contacts_nnz	intra_sum	intra_number_of_contacts	intra_number_of_contacts_nnz	intra_density	inter_left_intra_ratio	inter_right_intra_ratio	inter_left_inter_right_intra_ratio
 chr2	17100000	18100000	ID_0.01_10	-0.230354	.	0	148.64979	0	1.0	0	90	0	90	289.00809	100	100	1.0	0.0	0.5143447368549441	0.5143447368549441
 chr2	18100000	19100000	ID_0.01_11	-0.5135365	.	162.11248	211.04027000000002	1.0	1.0	100	140	100	140	277.9356	100	100	1.0	0.5832735353081793	0.7593135604075189	1.3425870957156982
diff --git a/tools/hicexplorer/test-data/hicInterIntraTAD/plot.png b/tools/hicexplorer/test-data/hicInterIntraTAD/plot.png
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diff --git a/tools/hicexplorer/test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf b/tools/hicexplorer/test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf
index 74988b86c78..e8e8fe0b9ac 100644
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diff --git a/tools/hicexplorer/test-data/hicPCA/pca1_test1.bw b/tools/hicexplorer/test-data/hicPCA/pca1_test1.bw
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diff --git a/tools/hicexplorer/test-data/hicPlotAverageRegions/defaults.png b/tools/hicexplorer/test-data/hicPlotAverageRegions/defaults.png
index 5b7497112f9..cde1894e1d2 100644
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diff --git a/tools/hicexplorer/test-data/hicPlotAverageRegions/defaults_log.png b/tools/hicexplorer/test-data/hicPlotAverageRegions/defaults_log.png
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diff --git a/tools/hicexplorer/test-data/hicPlotAverageRegions/defaults_log1p.png b/tools/hicexplorer/test-data/hicPlotAverageRegions/defaults_log1p.png
index 62e2b8bc7cd..56a4bf51f0c 100644
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diff --git a/tools/hicexplorer/test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png b/tools/hicexplorer/test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png
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diff --git a/tools/hicexplorer/test-data/hicPlotDistVsCounts_result1.png b/tools/hicexplorer/test-data/hicPlotDistVsCounts_result1.png
index e411b1aee67..1ac4c3bdefa 100644
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diff --git a/tools/hicexplorer/test-data/hicPlotDistVsCounts_result2.png b/tools/hicexplorer/test-data/hicPlotDistVsCounts_result2.png
index 29f5add1b9a..7577ed7d562 100644
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diff --git a/tools/hicexplorer/test-data/hicPlotMatrix/plot1.png b/tools/hicexplorer/test-data/hicPlotMatrix/plot1.png
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index 7b8dd7b73ab..59c60966ea6 100644
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-       <use xlink:href="#m7b986001a8" x="571.7" y="240.202362" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="240.202362" style="stroke: #000000; stroke-width: 0.8"/>
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@@ -677,7 +674,7 @@ z
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-       <use xlink:href="#m7b986001a8" x="571.7" y="189.229897" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="189.229897" style="stroke: #000000; stroke-width: 0.8"/>
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@@ -693,7 +690,7 @@ z
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       <g>
-       <use xlink:href="#m7b986001a8" x="571.7" y="138.257431" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="138.257431" style="stroke: #000000; stroke-width: 0.8"/>
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@@ -709,7 +706,7 @@ z
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       <g>
-       <use xlink:href="#m7b986001a8" x="571.7" y="87.284966" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="87.284966" style="stroke: #000000; stroke-width: 0.8"/>
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-       <use xlink:href="#m7b986001a8" x="571.7" y="36.3125" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="36.3125" style="stroke: #000000; stroke-width: 0.8"/>
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@@ -957,13 +954,13 @@ L 80.580682 461.675676
 L 75.996591 461.675676 
 L 71.4125 461.675676 
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-" clip-path="url(#p13ffe222dd)" style="fill: #1f77b4"/>
+" clip-path="url(#p11b451661a)" style="fill: #1f77b4"/>
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+       <use xlink:href="#m710e0e6472" x="71.4125" y="525.344717" style="stroke: #000000; stroke-width: 0.8"/>
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+       <use xlink:href="#m710e0e6472" x="71.4125" y="493.510197" style="stroke: #000000; stroke-width: 0.8"/>
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+       <use xlink:href="#m710e0e6472" x="71.4125" y="461.675676" style="stroke: #000000; stroke-width: 0.8"/>
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diff --git a/tools/hicexplorer/test-data/hicPlotSVL/p_values.txt b/tools/hicexplorer/test-data/hicPlotSVL/p_values.txt
index b310915539e..fe76a2efe4b 100644
--- a/tools/hicexplorer/test-data/hicPlotSVL/p_values.txt
+++ b/tools/hicexplorer/test-data/hicPlotSVL/p_values.txt
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.7.5
+# Created with HiCExplorer's hicPlotSVL 3.7.6
 # Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
 # Short range contacts: <= 2000000
 0_small_test_matrix.h5	1_small_test_matrix.h5	1.0
diff --git a/tools/hicexplorer/test-data/hicPlotSVL/plot.png b/tools/hicexplorer/test-data/hicPlotSVL/plot.png
index 406f1eea382..34d26afa2f8 100644
Binary files a/tools/hicexplorer/test-data/hicPlotSVL/plot.png and b/tools/hicexplorer/test-data/hicPlotSVL/plot.png differ
diff --git a/tools/hicexplorer/test-data/hicPlotSVL/ratios.txt b/tools/hicexplorer/test-data/hicPlotSVL/ratios.txt
index 54a19609687..d9b6851db83 100644
--- a/tools/hicexplorer/test-data/hicPlotSVL/ratios.txt
+++ b/tools/hicexplorer/test-data/hicPlotSVL/ratios.txt
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.7.5
+# Created with HiCExplorer's hicPlotSVL 3.7.6
 # Short range vs long range contacts per chromosome: raw data
 # Short range contacts: <= 2000000
 #	0_small_test_matrix.h5			1_small_test_matrix.h5
diff --git a/tools/hicexplorer/test-data/hicQuickQC/QC.log b/tools/hicexplorer/test-data/hicQuickQC/QC.log
index ea817f1d85b..2b152637577 100644
--- a/tools/hicexplorer/test-data/hicQuickQC/QC.log
+++ b/tools/hicexplorer/test-data/hicQuickQC/QC.log
@@ -1,5 +1,5 @@
 
-File	/tmp/tmpjkr0wi60/tmp/tmp8o_td4fd.h5		
+File	/tmp/tmpgf9pvov_/tmp/tmpovrpxt57.h5		
 Sequenced reads	983		
 Min rest. site distance	300		
 Max library insert size	1000		
diff --git a/tools/hicexplorer/test-data/hicValidateLocations/overlap_smc3_statistics b/tools/hicexplorer/test-data/hicValidateLocations/overlap_smc3_statistics
index a2700a521a6..1064b020bd5 100644
--- a/tools/hicexplorer/test-data/hicValidateLocations/overlap_smc3_statistics
+++ b/tools/hicexplorer/test-data/hicValidateLocations/overlap_smc3_statistics
@@ -1,5 +1,5 @@
-# HiCExplorer hicValidateLocations 3.7.5
-# Overlap of loop file /tmp/tmpjkr0wi60/files/a/f/1/dataset_af1f91e3-b1bd-4c1c-8842-935caae86bf2.dat with protein file /tmp/tmpjkr0wi60/files/e/6/e/dataset_e6e4503d-c6a1-4370-bc34-70b2fae3fc95.dat
+# HiCExplorer hicValidateLocations 3.7.6
+# Overlap of loop file /tmp/tmpgf9pvov_/files/2/9/c/dataset_29c1b4d3-8569-4405-ac40-08d8d9077d0d.dat with protein file /tmp/tmpgf9pvov_/files/4/8/3/dataset_48318067-0b54-463f-a9a7-9c751f3b7d1a.dat
 #
 Protein peaks: 3097
 Matched Loops: 530
diff --git a/tools/hicexplorer/test-data/li_viewpoint_32-33Mb.png b/tools/hicexplorer/test-data/li_viewpoint_32-33Mb.png
index 56ef9144057..2cb89035b11 100644
Binary files a/tools/hicexplorer/test-data/li_viewpoint_32-33Mb.png and b/tools/hicexplorer/test-data/li_viewpoint_32-33Mb.png differ
diff --git a/tools/hicexplorer/test-data/li_viewpoint_32Mb.png b/tools/hicexplorer/test-data/li_viewpoint_32Mb.png
index 17de07bf51c..8af18353127 100644
Binary files a/tools/hicexplorer/test-data/li_viewpoint_32Mb.png and b/tools/hicexplorer/test-data/li_viewpoint_32Mb.png differ
diff --git a/tools/hicexplorer/test-data/raw_qc_report_micro-c b/tools/hicexplorer/test-data/raw_qc_report_micro-c
new file mode 100644
index 00000000000..9e3dcd1c4f2
--- /dev/null
+++ b/tools/hicexplorer/test-data/raw_qc_report_micro-c
@@ -0,0 +1,24 @@
+
+File	matrix.cool		
+Sequenced reads	983		
+Max library insert size	1000		
+
+#	count	(percentage w.r.t. total sequenced reads)
+Pairs mappable, unique and high quality	300	(30.52)
+Hi-C contacts	215	(21.87)
+One mate unmapped	506	(51.48)
+One mate not unique	13	(1.32)
+Low mapping quality	164	(16.68)
+
+#	count	(percentage w.r.t. mappable, unique and high quality pairs)
+same fragment	85	(28.33)
+duplicated pairs	0	(0.00)
+
+#	count	(percentage w.r.t. total valid pairs used)
+inter chromosomal	24	(11.16)
+Intra short range (< 20kb)	61	(28.37)
+Intra long range (>= 20kb)	130	(60.47)
+Read pair type: inward pairs	42	(19.53)
+Read pair type: outward pairs	66	(30.70)
+Read pair type: left pairs	48	(22.33)
+Read pair type: right pairs	35	(16.28)
diff --git a/tools/hicexplorer/test-data/small_test_matrix_result_sorted.bam b/tools/hicexplorer/test-data/small_test_matrix_result_sorted.bam
index 59e87d46feb..9d8f4431e6a 100644
Binary files a/tools/hicexplorer/test-data/small_test_matrix_result_sorted.bam and b/tools/hicexplorer/test-data/small_test_matrix_result_sorted.bam differ
diff --git a/tools/hicexplorer/test-data/small_test_matrix_result_sorted_microc.bam b/tools/hicexplorer/test-data/small_test_matrix_result_sorted_microc.bam
new file mode 100644
index 00000000000..9d8f4431e6a
Binary files /dev/null and b/tools/hicexplorer/test-data/small_test_matrix_result_sorted_microc.bam differ