diff --git a/openbr/core/core.cpp b/openbr/core/core.cpp
index 6260193..94b9263 100644
--- a/openbr/core/core.cpp
+++ b/openbr/core/core.cpp
@@ -47,12 +47,12 @@ struct AlgorithmCore
         qDebug("Training on %s%s", qPrintable(input.flat()),
                model.isEmpty() ? "" : qPrintable(" to " + model));
 
-        QScopedPointer<Transform> trainingWrapper(Transform::make("DirectStream([Identity], readMode=DistributeFrames)", NULL));
+        QScopedPointer<Transform> trainingWrapper(Transform::make("DirectStream(readMode=DistributeFrames)", NULL));
 
         CompositeTransform * downcast = dynamic_cast<CompositeTransform *>(trainingWrapper.data());
         if (downcast == NULL)
             qFatal("downcast failed?");
-        downcast->transforms[0] = this->transform.data();
+        downcast->transforms.append(this->transform.data());
 
         downcast->init();
 
@@ -163,14 +163,14 @@ struct AlgorithmCore
 
         if (!multiProcess)
         {
-            QString pipeDesc = "Identity+GalleryOutput("+gallery.flat()+")+ProgressCounter("+QString::number(data.length())+")+Discard";
+            QString pipeDesc = "GalleryOutput("+gallery.flat()+")+ProgressCounter("+QString::number(data.length())+")+Discard";
             basePipe.reset(Transform::make(pipeDesc,NULL));
             CompositeTransform * downcast = dynamic_cast<CompositeTransform *>(basePipe.data());
             if (downcast == NULL)
                 qFatal("downcast failed?");
 
             // replace that placeholder with the current algorithm
-            downcast->transforms[0] = this->transform.data();
+            downcast->transforms.prepend(this->transform.data());
 
             // call init on the pipe to collapse the algorithm (if its top level is a pipe)
             downcast->init();
@@ -182,7 +182,7 @@ struct AlgorithmCore
         }
 
         // Next, we make a Stream (with placeholder transform)
-        QString streamDesc = "Stream(Identity, readMode=DistributeFrames)";
+        QString streamDesc = "Stream(readMode=DistributeFrames)";
         QScopedPointer<Transform> baseStream(Transform::make(streamDesc, NULL));
         WrapperTransform * wrapper = dynamic_cast<WrapperTransform *> (baseStream.data());
 
@@ -322,72 +322,194 @@ struct AlgorithmCore
         if (distance->compare(targetGallery, queryGallery, output))
             return;
 
-        if (output.exists() && output.get<bool>("cache")) return;
+        // Are we comparing the same gallery against itself?
+        bool selfCompare = targetGallery == queryGallery;
+
+        // Should we use multiple processes to do enrollment/comparison? If not, we just do multi-threading.
+        bool multiProcess = Globals->file.getBool("multiProcess", false);
+
+        // In comparing two galleries, we will keep the smaller one in memory, and load the larger one
+        // incrementally. If the gallery set is larger than the probe set, we operate in transpose mode
+        // i.e. we must transpose our output, to still write the output matrix in row-major order.
+        bool transposeMode = false;
+
+        // Is the larger gallery already enrolled? If not, we will enroll those images in-line with their
+        // comparison against the smaller gallery (which will be enrolled, and stored in memory).
+        bool needEnrollRows = false;
+
+
+
+
+        if (output.exists() && output.get<bool>("cache", false)) return;
         if (queryGallery == ".") queryGallery = targetGallery;
 
-        QScopedPointer<Gallery> t, q;
-        FileList targetFiles, queryFiles;
-        retrieveOrEnroll(targetGallery, t, targetFiles);
-        retrieveOrEnroll(queryGallery, q, queryFiles);
 
-        QList<int> partitionSizes;
-        QList<File> outputFiles;
-        if (output.contains("split")) {
-            if (!output.fileName().contains("%1")) qFatal("Output file name missing split number place marker (%%1)");
-            partitionSizes = output.getList<int>("split");
-            for (int i=0; i<partitionSizes.size(); i++) {
-                File splitOutputFile = output.name.arg(i);
-                outputFiles.append(splitOutputFile);
-            }
-        } else {
-            outputFiles.append(output);
+        // To decide which gallery is larger, we need to read both, but at this point we just want the
+        // metadata, and don't need the enrolled matrices.
+        FileList targetMetadata;
+        FileList queryMetadata;
+
+        // Emptyread reads a gallery, and discards any matrices present, keeping only the metadata.
+        targetMetadata = FileList::fromGallery(targetGallery, true);
+        queryMetadata  = FileList::fromGallery(queryGallery, true);
+
+
+        // Is the target or query set larger? We will use the larger as the rows of our comparison matrix (and transpose the output if necessary)
+        transposeMode = targetMetadata.size() > queryMetadata.size();
+
+        File rowGallery = queryGallery;
+        File colGallery = targetGallery;
+        int rowSize = queryMetadata.size();
+
+        if (transposeMode)
+        {
+            rowGallery = targetGallery;
+            colGallery = queryGallery;
+            rowSize = targetMetadata.size();
         }
 
-        QList<Output*> outputs;
-        foreach (const File &outputFile, outputFiles)
-            outputs.append(Output::make(outputFile, targetFiles, queryFiles));
 
-        if (distance.isNull()) qFatal("Null distance.");
-        Globals->currentStep = 0;
-        Globals->totalSteps = double(targetFiles.size()) * double(queryFiles.size());
-        Globals->startTime.start();
+        // Is the column gallery already enrolled? We keep the enrolled column gallery in memory, and in multi-process
+        // mode, every worker process retains a copy of this gallery in memory. When not in multi-process mode, we can
+        // simple make sure the enrolled data is stored in a memGallery, but in multi-process mode we save the enrolled
+        // data to disk (as a .gal file) so that each worker process can read it without re-doing enrollment.
+        File colEnrolledGallery = colGallery;
+        QString targetExtension = multiProcess ? "gal" : "mem";
+
+        // If the column gallery is not already of the appropriate type, we need to do something
+        if (colGallery.suffix() != targetExtension)
+        {
+            // Build the name of a gallery containing the enrolled data, of the appropriate type.
+            colEnrolledGallery = colGallery.baseName() + colGallery.hash() + (multiProcess ? ".gal" : ".mem");
 
-        int queryBlock = -1;
-        bool queryDone = false;
-        while (!queryDone) {
-            queryBlock++;
-            TemplateList queries = q->readBlock(&queryDone);
+            // Check if we have to do real enrollment, and not just convert the gallery's type.
+            if (!(QStringList() << "gal" << "template" << "mem").contains(colGallery.suffix()))
+            {
+                enroll(colGallery, colEnrolledGallery);
+            }
+            // If the gallery does have enrolled templates, but is not the right type, we do a simple
+            // type conversion for it.
+            else
+            {
+                QScopedPointer<Gallery> readColGallery(Gallery::make(colGallery));
+                TemplateList templates = readColGallery->read();
+                QScopedPointer<Gallery> enrolledColOutput(Gallery::make(colEnrolledGallery));
+                enrolledColOutput->writeBlock(templates);
+            }
+        }
+
+        // We have handled the column gallery, now decide whehter or not we have to enroll the row gallery.
+        if (selfCompare)
+        {
+            // For self-comparisons, we just use the already enrolled column set.
+            rowGallery = colEnrolledGallery;
+        }
+        // Otherwise, we will need to enroll the row set. Since the actual comparison is defined via a transform
+        // which compares incoming templates against a gallery, we will handle enrollment of the row set by simply
+        // building a transform that does enrollment (using the current algorithm), then does the comparison in one
+        // step. This way, we don't have to retain the complete enrolled row gallery in memory, or on disk.
+        else if(!(QStringList() << "gal" << "mem" << "template").contains(rowGallery.suffix()))
+        {
+            needEnrollRows = true;
+        }
 
-            QList<TemplateList> queryPartitions;
-            if (!partitionSizes.empty()) queryPartitions = queries.partition(partitionSizes);
-            else queryPartitions.append(queries);
+        // At this point, we have decided how we will structure the comparison (either in transpose mode, or not), 
+        // and have the column gallery enrolled, and have decided whether or not we need to enroll the row gallery.
+        // From this point, we will build a single algorithm that (optionally) does enrollment, then does comparisons
+        // and output, optionally using ProcessWrapper to do the enrollment and comparison in separate processes.
+        //
+        // There are two main components to this algorithm. The first is the (optional) enrollment and then the
+        // comparison step (built from a GalleryCompare transform), and the second is the sequential matrix output and
+        // progress counting step.
+        // After the base algorithm is built, the whole thing will be run in a stream, so that I/O can be handled sequentially.
 
-            for (int i=0; i<queryPartitions.size(); i++) {
-                int targetBlock = -1;
-                bool targetDone = false;
-                while (!targetDone) {
-                    targetBlock++;
 
-                    TemplateList targets = t->readBlock(&targetDone);
 
-                    QList<TemplateList> targetPartitions;
-                    if (!partitionSizes.empty()) targetPartitions = targets.partition(partitionSizes);
-                    else targetPartitions.append(targets);
+        // The actual comparison step is done by a GalleryCompare transform, which has a Distance, and a gallery as data.
+        // Incoming templates are compared against the templates in the gallery, and the output is the resulting score
+        // vector.
+        QString compareRegionDesc = "Pipe([GalleryCompare("+Globals->algorithm + "," + colEnrolledGallery.flat() + ")])";
 
-                    outputs[i]->setBlock(queryBlock, targetBlock);
-                    distance->compare(targetPartitions[i], queryPartitions[i], outputs[i]);
 
-                    Globals->currentStep += double(targets.size()) * double(queries.size());
-                    Globals->printStatus();
-                }
+        QScopedPointer<Transform> compareRegion;
+        // If we need to enroll the row set, we add the current algorithm's enrollment transform before the
+        // GalleryCompare in a pipe.
+        if (needEnrollRows)
+        {
+            if (!multiProcess)
+            {
+                compareRegionDesc = compareRegionDesc;
+                compareRegion.reset(Transform::make(compareRegionDesc,NULL));
+                CompositeTransform * downcast = dynamic_cast<CompositeTransform *> (compareRegion.data());
+                if (downcast == NULL)
+                    qFatal("Pipe downcast failed in compare");
+
+                downcast->transforms.prepend(this->transform.data());
+                downcast->init();
             }
+            else
+            {
+                compareRegionDesc = "ProcessWrapper(" + this->transformString + "+" + compareRegionDesc + ")";
+                compareRegion.reset(Transform::make(compareRegionDesc, NULL));
+            }
+        }
+        else {
+            if (multiProcess)
+                compareRegionDesc = "ProcessWrapper(" + compareRegionDesc + ")";
+            compareRegion.reset(Transform::make(compareRegionDesc,NULL));
         }
 
-        qDeleteAll(outputs);
+        // At this point, compareRegion is a transform, which optionally does enrollment, then compares the row
+        // set against the column set. If in multi-process mode, the enrollment and comparison are wrapped in a 
+        // ProcessWrapper transform, and will be transparently run in multiple processes.
+        compareRegion->init();
+
+
+        // We also need to add Output and progress counting to the algorithm we are building, so we will assign them to
+        // two stages of a pipe.
+        QString joinDesc = "Pipe()";
+        QScopedPointer<Transform> join(Transform::make(joinDesc, NULL));
+
+        // The output transform takes the metadata memGalleries we set up previously as input, along with the
+        // output specification we were passed. Gallery metadata is necessary for some Outputs to function correctly.
+        QString outputString = output.flat().isEmpty() ? "Empty" : output.flat();
+        QString outputRegionDesc = "Output("+ outputString +"," + targetGallery.flat() +"," + queryGallery.flat() + ","+ QString::number(transposeMode ? 1 : 0) + ")";
+        // The ProgressCounter transform will simply provide a display about the number of rows completed.
+        outputRegionDesc += "+ProgressCounter("+QString::number(rowSize)+")+Discard";
+        QScopedPointer<Transform> outputTform(Transform::make(outputRegionDesc, NULL));
+
+        // Assign the comparison transform we previously built, and the output transform  we just built to
+        // two stages of a pipe.
+        CompositeTransform * downcast = dynamic_cast<CompositeTransform *> (join.data());
+        downcast->transforms.append(compareRegion.data());
+        downcast->transforms.append(outputTform.data());
+
+        // With this, we have set up a transform which (optionally) enrolls templates, compares them
+        // against a gallery, and outputs them.
+        join->init();
+
+        // Now, we will give that base transform to a stream, which will incrementally read the row gallery
+        // and pass the transforms it reads through the base algorithm.
+        QString streamDesc = "Stream(readMode=StreamGallery)";
+        QScopedPointer<Transform> streamBase(Transform::make(streamDesc, NULL));
+        WrapperTransform * streamWrapper = dynamic_cast<WrapperTransform *> (streamBase.data());
+        streamWrapper->transform = join.data();
+
+        // The transform we will use is now complete.
+        streamWrapper->init();
+
+        // We set up a template containing the rowGallery we want to compare. 
+        TemplateList rowGalleryTemplate;
+        rowGalleryTemplate.append(Template(rowGallery));
+        TemplateList outputGallery;
+
+        // Set up progress counting variables
+        Globals->currentStep = 0;
+        Globals->totalSteps = rowSize;
+        Globals->startTime.start();
 
-        const float speed = 1000 * Globals->totalSteps / Globals->startTime.elapsed() / std::max(1, abs(Globals->parallelism));
-        if (!Globals->quiet && (Globals->totalSteps > 1)) fprintf(stderr, "\rSPEED=%.1e  \n", speed);
-        Globals->totalSteps = 0;
+        // Do the actual comparisons
+        streamWrapper->projectUpdate(rowGalleryTemplate, outputGallery);
     }
 
 private:
@@ -584,7 +706,7 @@ QSharedPointer<br::Transform> br::Transform::fromAlgorithm(const QString &algori
         return AlgorithmManager::getAlgorithm(algorithm)->transform;
     else {
         QSharedPointer<Transform> orig_tform = AlgorithmManager::getAlgorithm(algorithm)->transform;
-        QSharedPointer<Transform> newRoot = QSharedPointer<Transform>(Transform::make("Stream(Identity)", NULL));
+        QSharedPointer<Transform> newRoot = QSharedPointer<Transform>(Transform::make("Stream(readMode=DistributeFrames)", NULL));
         WrapperTransform * downcast = dynamic_cast<WrapperTransform *> (newRoot.data());
         downcast->transform = orig_tform.data();
         downcast->init();
@@ -597,4 +719,5 @@ QSharedPointer<br::Distance> br::Distance::fromAlgorithm(const QString &algorith
     return AlgorithmManager::getAlgorithm(algorithm)->distance;
 }
 
+
 #include "core.moc"
diff --git a/openbr/openbr_plugin.h b/openbr/openbr_plugin.h
index e17a70c..dabbc80 100644
--- a/openbr/openbr_plugin.h
+++ b/openbr/openbr_plugin.h
@@ -369,6 +369,8 @@ struct BR_EXPORT FileList : public QList<File>
 
     QList<int> crossValidationPartitions() const; /*!< \brief Returns the cross-validation partition (default=0) for each file in the list. */
     int failures() const; /*!< \brief Returns the number of files with br::File::failed(). */
+
+    static FileList fromGallery(const File &gallery, bool cache = false); /*!< \brief Create a file list from a br::Gallery. */
 };
 
 /*!
diff --git a/openbr/plugins/distance.cpp b/openbr/plugins/distance.cpp
index 214be02..af3a8b0 100644
--- a/openbr/plugins/distance.cpp
+++ b/openbr/plugins/distance.cpp
@@ -488,6 +488,8 @@ class GalleryCompareTransform : public Transform
             distance = Distance::fromAlgorithm(distanceAlgorithm);
         }
     }
+public:
+    GalleryCompareTransform() : Transform(false, false) {}
 };
 
 BR_REGISTER(Transform, GalleryCompareTransform)
diff --git a/openbr/plugins/gallery.cpp b/openbr/plugins/gallery.cpp
index e1e2144..5b0c2a6 100644
--- a/openbr/plugins/gallery.cpp
+++ b/openbr/plugins/gallery.cpp
@@ -393,6 +393,51 @@ class memGallery : public Gallery
 
 BR_REGISTER(Gallery, memGallery)
 
+FileList FileList::fromGallery(const File & file, bool cache)
+{
+    File targetMeta = file;
+    targetMeta.name = targetMeta.path() + targetMeta.baseName() + "_meta" + targetMeta.hash() + ".mem";
+
+    FileList fileData;
+
+    // Did we already read the data?
+    if (MemoryGalleries::galleries.contains(targetMeta))
+    {
+        return MemoryGalleries::galleries[targetMeta].files();
+    }
+
+    TemplateList templates;
+    // OK we read the data in some form, does the gallery type containing matrices?
+    if ((QStringList() << "gal" << "mem" << "template").contains(file.suffix())) {
+        // Retrieve it block by block, dropping matrices from read templates.
+        QScopedPointer<Gallery> gallery(Gallery::make(file));
+        gallery->set_readBlockSize(10);
+        bool done = false;
+        while (!done)
+        {
+            TemplateList tList = gallery->readBlock(&done);
+            for (int i=0; i < tList.size();i++)
+            {
+                tList[i].clear();
+                templates.append(tList[i].file);
+            }
+        }
+    }
+    else {
+        // this is a gallery format that doesn't include matrices, so we can just read it
+        QScopedPointer<Gallery> gallery(Gallery::make(file));
+        templates= gallery->read();
+    }
+
+    if (cache)
+    {
+        QScopedPointer<Gallery> memOutput(Gallery::make(targetMeta));
+        memOutput->writeBlock(templates);
+    }
+    fileData = templates.files();
+    return fileData;
+}
+
 /*!
  * \ingroup galleries
  * \brief Treats each line as a file.
diff --git a/openbr/plugins/misc.cpp b/openbr/plugins/misc.cpp
index eee78ca..72cb01a 100644
--- a/openbr/plugins/misc.cpp
+++ b/openbr/plugins/misc.cpp
@@ -636,11 +636,8 @@ class OutputTransform : public TimeVaryingTransform
         if (targetName.isEmpty() || queryName.isEmpty() || outputString.isEmpty())
             return;
 
-        QScopedPointer<Gallery> tGallery(Gallery::make(targetName));
-        QScopedPointer<Gallery> qGallery(Gallery::make(queryName));
-
-        FileList targetFiles = tGallery->files();
-        FileList queryFiles  = qGallery->files();
+        FileList targetFiles = FileList::fromGallery(targetName);
+        FileList queryFiles  = FileList::fromGallery(queryName);
 
         currentBlockRow = 0;
         currentBlockCol = 0;