diff --git a/README.rst b/README.rst
index 9d76ee69..92fd02a6 100644
--- a/README.rst
+++ b/README.rst
@@ -18,29 +18,34 @@ If you want us to add a single cell dataset to the website http://cells.ucsc.edu
 please contact us at cells@ucsc.edu. We are happy to add any dataset.
 
 This is a viewer for a static, precomputed layout. If you're looking for an interative layout, where you can 
-move the cells around and run algorithsm interactively, try Chan-Zuckerberg's own cellxgene or Spring.
-Another viewer is `Scope <http://scope.aertslab.org/>`_.
+move the cells around and run some algorithms interactively, try Chan-Zuckerberg's own cellxgene or Spring.
+A website with both datasets and some analysis is `Scope <http://scope.aertslab.org/>`_.
 
-Apart from labs at UCSC, UCSF and Gladstone who host their data at
-cells.ucsc.edu, other groups have setup their own cell browsers:
+Many labs host their data at cells.ucsc.edu by sending it to us, but some groups have setup their own cell browsers:
 
 * Alexander Misharin Lab, Northwester University, https://www.nupulmonary.org/resources/
 * Accelerating Medicine Partnership Consortium, https://immunogenomics.io/cellbrowser/, used in `Zhang et al. 2018 <https://www.biorxiv.org/content/10.1101/351130v1>`_ and `Der et al 2018 <https://www.biorxiv.org/content/10.1101/382846v1>`_
-* Sansom Lab, Oxford, https://sansomlab.github.io
-* http://caire.ipmc.cnrs.fr/cellbrowser/Differentiation/ Zaragosi group at IPMC CNRS Nice, for the manuscript https://dev.biologists.org/content/early/2019/09/25/dev.177428.abstract
+* Sansom Lab, Oxford, https://sansomlab.github.io for `Croft et al, Nature 2019 <https://www.nature.com/articles/s41586-019-1263-7>`_
+* http://caire.ipmc.cnrs.fr/cellbrowser/Differentiation/ (URL has changed, contacted authors) Zaragosi group at IPMC CNRS Nice, for the manuscript https://dev.biologists.org/content/early/2019/09/25/dev.177428.abstract
+
+These papers have cell browsers made at UCSC:
+* organoidatlas: https://www.sciencedirect.com/science/article/pii/S221112472030053X
+* dros-brain: https://elifesciences.org/articles/50354
+* kidney-atlas: https://science.sciencemag.org/content/365/6460/1461.abstract
+* allen-celltypes/mouse-cortex: https://www.biorxiv.org/content/10.1101/2020.03.30.015214v1.full
+* organoidreportcard: https://www.nature.com/articles/s41586-020-1962-0
 
 Additional availability
 -----------------------
 
-* The preferred installation is via pip https://pypi.org/project/cellbrowser/0.4.12/, see https://cellbrowser.readthedocs.io
-* Bioconda: this tool is available to install via `bioconda <https://bioconda.github.io/recipes/ucsc-cell-browser/README.html>`_Note that the conda release is usually a bit outdated relative to the pip release. 
+* The preferred installation is via pip https://pypi.org/project/cellbrowser/, for documentation see https://cellbrowser.readthedocs.io
+* Bioconda: this tool is available to install via `bioconda <https://bioconda.github.io/recipes/ucsc-cell-browser/README.html>`_. Note that the conda release is usually a bit outdated relative to the pip release, so use pip if possible. If you cannot use pip, please contact us. 
 * Biocontainers: there is a biocontainer automatically generated from the bioconda package available `here <https://quay.io/repository/biocontainers/ucsc-cell-browser>`_
 * The Seurat3Wizard, demo at http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard, builds a cell browser as its last step
 * Galaxy: there is a Galaxy tool for UCSC CellBrowser, which can be installed on any Galaxy instance via its `Galaxy Toolshed entry <https://toolshed.g2.bx.psu.edu/view/ebi-gxa/ucsc_cell_browser>`_ or it can be directly used by users at the `Human Cell Atlas Galaxy instance <https://humancellatlas.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/ebi-gxa/ucsc_cell_browser/ucsc_cell_browser>`_ or as part of the example workflows, such as the `Human Cell Atlas / Scanpy CellBrowser workflow <https://humancellatlas.usegalaxy.eu/u/pmoreno/w/humancellatlas-scanpy-cellbrowser>`_ or the `EBI Single Cell Expression Atlas / Scanpy / CellBrowser workflow <https://humancellatlas.usegalaxy.eu/u/pmoreno/w/atlas-scanpy-cellbrowser-imported-from-uploaded-file>`_
 
-
-Funded by the California Institute of Regenerative Medicine and the
-Chan-Zuckerberg Initiative https://www.chanzuckerberg.com/.
+This project was funded by the California Institute of Regenerative Medicine and the
+Chan-Zuckerberg Initiative https://www.chanzuckerberg.com/. In 2020, it is funded through a supplement to the NHGRI Genome Browser grant.
 
 This is early research software. You are likely to find bugs. Please open a Github
 ticket or email us at cells@ucsc.edu, we can usually fix them quickly.
diff --git a/docs/cellBrowserLogo.png b/docs/cellBrowserLogo.png
new file mode 100644
index 00000000..0d05b701
Binary files /dev/null and b/docs/cellBrowserLogo.png differ
diff --git a/docs/cellBrowserLogoBallOnly.png b/docs/cellBrowserLogoBallOnly.png
new file mode 100644
index 00000000..701e2cc2
Binary files /dev/null and b/docs/cellBrowserLogoBallOnly.png differ
diff --git a/src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js b/src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js
index a5bb482f..436c7b23 100644
--- a/src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js
+++ b/src/cbPyLib/cellbrowser/cbWeb/js/cellBrowser.js
@@ -31,6 +31,8 @@ var cellbrowser = function() {
 
     var renderer = null;
 
+    var background = null;
+
     // last 10 genes
     var gRecentGenes = [];
 
@@ -932,7 +934,7 @@ var cellbrowser = function() {
 
         let doFaceting = false;
         let filtList = [];
-        if (openDsInfo.parents === undefined) {
+        if (openDsInfo.parents === undefined && openDsInfo.datasets !== undefined) {
             //noteLines.push("<span>Filter:</span>");
             let bodyParts = getBodyParts(openDsInfo.datasets);
             if (bodyParts.length!==0) {
@@ -1055,7 +1057,9 @@ var cellbrowser = function() {
             changeUrl({"ds":openDatasetName});
         });
 
+        var focused = document.activeElement;
         var scroller = $("#tpDatasetList").overlayScrollbars({ });
+        $(focused).focus();
 
 
         $("#tabLink1").tab("show");
@@ -1074,11 +1078,16 @@ var cellbrowser = function() {
     }
 
 
-    function onSelChange(cellIds) {
+    function onSelChange(selection) {
     /* called each time when the selection has been changed */
+        var cellIds = [];
+        selection.forEach(function(x) {cellIds.push(x)});
+        $("#tpSetBackground").parent("li").removeClass("disabled");
+
         if (cellIds.length===0 || cellIds===null) {
             clearMetaAndGene();
             clearSelectionState();
+            $("#tpSetBackground").parent("li").addClass("disabled");
         } else if (cellIds.length===1) {
             var cellId = cellIds[0];
             var cellCountBelow = cellIds.length-1;
@@ -1093,6 +1102,22 @@ var cellbrowser = function() {
         if ("geneSym" in gLegend)
             buildViolinPlot();
 
+        var cols = renderer.col.arr;
+        var selectedLegends = {};
+        for (var i = 0; i < gLegend.rows.length; i++) {
+            selectedLegends[i] = 0;
+        }
+        selection.forEach(function(cellId) {
+            selectedLegends[cols[cellId]]++;
+        });
+        for (var i = 0; i < gLegend.rows.length; i++) {
+            if (selectedLegends[i] == gLegend.rows[i].count) {
+                $("#tpLegendCheckbox_" + i).prop("checked", true);
+            } else {
+                $("#tpLegendCheckbox_" + i).prop("checked", false);
+            }
+        }
+        updateLegendGrandCheckbox();
     }
 
     function onSaveAsClick() {
@@ -1506,6 +1531,26 @@ var cellbrowser = function() {
         return true;
     }
 
+    function onBackgroudSetClick() {
+// Tools -> Set cells as background
+        if ($("#tpSetBackground").parent("li").hasClass("disabled")) {
+            return;
+        }
+
+        background = renderer.getSelection();
+        $("#tpResetBackground").parent("li").removeClass("disabled");
+        if ("geneSym" in gLegend)
+            buildViolinPlot();
+    }
+
+    function onBackgroudResetClick() {
+// Tools -> Reset background cells
+        background = null;
+        $("#tpResetBackground").parent("li").addClass("disabled");
+        if ("geneSym" in gLegend)
+            buildViolinPlot();
+    }
+
     function saveQueryList(queryList) {
         var queryStr = JSURL.stringify(queryList);
         changeUrl({'select':queryStr});
@@ -2154,6 +2199,8 @@ var cellbrowser = function() {
          //htmls.push('<li><a href="#" id="tpRenameClusters">Rename clusters...<span class="dropmenu-item-content"></span></a></li>');
          htmls.push('<li><a href="#" id="tpCustomAnnots">Remove all custom annotations<span class="dropmenu-item-content"></span></a></li>');
          //htmls.push('<li><a href="#" id="tpCluster">Run clustering...<span class="dropmenu-item-content"></span></a></li>');
+         htmls.push('<li class="disabled"><a href="#" id="tpSetBackground">Set as background cells<span class="dropmenu-item-content">b s</span></a></li>');
+         htmls.push('<li class="disabled"><a href="#" id="tpResetBackground">Reset background cells<span class="dropmenu-item-content">b r</span></a></li>');
          htmls.push('</ul>'); // Tools dropdown-menu
          htmls.push('</li>'); // Tools dropdown container
 
@@ -2203,6 +2250,8 @@ var cellbrowser = function() {
 
        $('#tpRenameClusters').click( onRenameClustersClick );
        $('#tpCustomAnnots').click( onCustomAnnotationsClick );
+       $('#tpSetBackground').click( onBackgroudSetClick );
+       $('#tpResetBackground').click( onBackgroudResetClick );
        //$('#tpCluster').click( onRunClusteringClick );
 
        // This version is more like OSX/Windows:
@@ -2480,10 +2529,13 @@ var cellbrowser = function() {
 
         var labelLines = [];
         //labelLines.push([labelList[0], dataList[0].length+" cells"]);
-        labelLines.push([labelList[0], dataList[0].length]);
-        if (dataList.length > 1)
+        labelLines[0] = labelList[0].split("\n");
+        labelLines[0].push(dataList[0].length);
+        if (dataList.length > 1) {
             //labelLines.push([labelList[1], dataList[1].length+" cells"]);
-            labelLines.push([labelList[1], dataList[1].length]);
+            labelLines[1] = labelList[1].split("\n");
+            labelLines[1].push(dataList[1].length);
+        }
 
         const ctx = document.getElementById("tpViolinCanvas").getContext("2d");
 
@@ -2566,6 +2618,31 @@ var cellbrowser = function() {
         var dataList = [];
         var labelList = [];
         var selCells = renderer.getSelection();
+
+        // filter exprVec by background
+        if (background !== null) {
+            var ourSelCells = {};
+            for (var i = 0; i < selCells.length; i++) {
+                ourSelCells[selCells[i]] = true;
+            }
+            var ourCells = {};
+            for (i = 0; i < background.length; i++) {
+                ourCells[background[i]] = true;
+            }
+
+            var result = [];
+            var renamedSelCells = [];
+            for (i = 0; i < exprVec.length; i++) {
+                if (i in ourSelCells) {
+                    renamedSelCells.push(result.length);
+                    result.push(exprVec[i]);
+                } else if (i in ourCells) {
+                    result.push(exprVec[i]);
+                }
+            }
+            exprVec = result;
+            selCells = renamedSelCells;
+        }
         // if we have a violin meta field to split on, make two violin plots, one meta vs, the other meta
         // restrict the plot to the selected cells, if any
         if (db.conf.violinField!==undefined) {
@@ -2575,12 +2652,20 @@ var cellbrowser = function() {
             if (selCells.length===0) {
                 // no selection, no violinField: default to a single violin plot
                 dataList = [Array.prototype.slice.call(exprVec)];
-                labelList = ['All cells'];
+                if (background === null) {
+                    labelList = ['All cells'];
+                } else {
+                    labelList = ['Background\ncells'];
+                }
                 buildViolinFromValues(labelList, dataList);
             } else {
                 // cells are selected and no violin field: make two violin plots, selected against other cells
                 dataList = splitExpr(exprVec, selCells);
-                labelList = ['Selected', 'Others'];
+                if (background === null) {
+                    labelList = ['Selected', 'Others'];
+                } else {
+                    labelList = ['Selected', 'Background\nOthers'];
+                }
                 if (dataList[1].length===0) {
                     dataList = [dataList[0]];
                     labelList = ['All Selected'];
@@ -3296,6 +3381,7 @@ var cellbrowser = function() {
         gLegend.rowType = "range";
         gLegend.exprVec = exprVec; // raw expression values, e.g. floats
         gLegend.decExprVec = decExprVec; // expression values as deciles, array of bytes
+        gLegend.selectionDirection = "all";
         legendSetPalette(gLegend, "default");
 
         var colors = legendGetColors(legendRows);
@@ -3841,6 +3927,7 @@ var cellbrowser = function() {
         legend.rows = rows;
         legend.isSortedByName = sortResult.isSortedByName;
         legend.rowType = "category";
+        legend.selectionDirection = "all";
         legendSetPalette(legend, "default");
         return legend;
     }
@@ -4865,6 +4952,8 @@ var cellbrowser = function() {
         Mousetrap.bind('s i', onSelectInvertClick);
         Mousetrap.bind('s s', onSelectNameClick);
 
+        Mousetrap.bind('b s', onBackgroudSetClick);
+        Mousetrap.bind('b r', onBackgroudResetClick);
 
         Mousetrap.bind('m', function() {$('#tpMetaCombo').trigger("chosen:open"); return false;});
         Mousetrap.bind('d', function() {$('#tpDatasetCombo').trigger("chosen:open"); return false;});
@@ -5080,49 +5169,9 @@ var cellbrowser = function() {
     function onLegendLabelClick(ev) {
     /* called when user clicks on legend entry. */
 
-        //function saveLabel() {
-            ///* save the current labelEl text to the cart and update everything */
-            //$(".tooltip").remove(); // not sure why tooltips won't disappear here
-            //labelEl.removeAttr("contenteditable");
-            //var newLabel = labelEl.text(); // = strip the rich text tags possibly added through copy/paste
-            //var metaInfo = gLegend.metaInfo;
-            //cartFieldArrayUpdate(db, metaInfo, "shortLabels", legendId, newLabel);
-            //legendUpdateLabels(gLegend.metaInfo.name);
-            //rendererUpdateLabels(metaInfo);
-            //buildLegendBar();
-            //renderer.drawDots();
-        //}
-
         var legendId = parseInt(ev.target.id.split("_")[1]);
         var colorIndex = gLegend.rows[legendId].intKey;
-
-        //if (("lastClicked" in gLegend) && gLegend.lastClicked===legendId) {
-            // user clicked the same entry as before: 
-            //gLegend.lastClicked = null;
-                //$('#tpLegend_'+legendId).removeClass('tpLegendSelect');
-                //renderer.selectClear();
-        //}
-        //else {
-            // clear the old selection
-            //if (!ev.shiftKey && !ev.ctrlKey && !ev.metaKey) {
-                //renderer.selectClear();
-                //$('.tpLegend').removeClass('tpLegendSelect');
-            //}
-            $("#tpLegendCheckbox_"+colorIndex).prop("checked", true);
-            renderer.selectByColor(colorIndex);
-            //menuBarShow("#tpFilterButton");
-            //menuBarShow("#tpOnlySelectedButton");
-            //$('#tpLegend_'+legendId).addClass('tpLegendSelect');
-            //gLegend.lastClicked=legendId;
-            clearSelectionState();
-            //if (gLegend.type==="meta" && gLegend.metaInfo.type==="enum") {
-                //let fieldName = gLegend.metaInfo.name;
-                //let fieldVal = gLegend.metaInfo.valCounts[colorIndex][0];
-                //let queryList = [{"m":fieldName, "eq":fieldVal}];
-                //saveQueryList(queryList);
-            //}
-        //}
-        renderer.drawDots();
+        $("#tpLegendCheckbox_" + colorIndex).click();
     }
 
     function onSortByClick (ev) {
@@ -5179,25 +5228,47 @@ var cellbrowser = function() {
     function setLegendHeaders(type) {
     /* set the headers of the right-hand legend */
         if (type==="category") {
-            $('#tpLegendCol1').html('<span title="unselect all checkboxes below" id="tpLegendClear">&#9746;</span><span class="tpLegendHover" title="click to sort by name"> Name<span class="caret"></span></span>');
+            $('#tpLegendCol1').html('<span title="select all checkboxes below" id="tpLegendClear">&#9745;</span><span class="tpLegendHover" title="click to sort by name"> Name<span class="caret"></span></span>');
             $('#tpLegendCol2').html('<span class="tpLegendHover" title="click to sort by frequency"> Frequency<span class="caret"></span></span>');
         }
         else {
-            $('#tpLegendCol1').html('<span title="unselect all checkboxes below" id="tpLegendClear">&#9746;</span> Range<span');
+            $('#tpLegendCol1').html('<span title="select all checkboxes below" id="tpLegendClear">&#9745;</span> Range<span');
             $('#tpLegendCol2').html('Frequency');
         }
         activateTooltip("#tpLegendClear");
         activateTooltip(".tpLegendHover");
     }
 
+    function updateLegendGrandCheckbox() {
+        var checkbox = $("#tpLegendClear");
+        var total = renderer.getCount();
+        var selected = renderer.selCells.size;
+        if (gLegend.selectionDirection == "all" && total == selected) {
+            gLegend.selectionDirection = "none";
+            checkbox.html("&#9746;");
+            // from https://stackoverflow.com/questions/9501921/change-twitter-bootstrap-tooltip-content-on-click
+            checkbox.attr('title', "unselect all checkboxes below")
+                .bsTooltip('fixTitle')
+                .data('bs.tooltip')
+                .$tip.find('.tooltip-inner')
+                .text("unselect all checkboxes below");
+        } else if (gLegend.selectionDirection == "none" && selected === 0) {
+            gLegend.selectionDirection = "all";
+            checkbox.html("&#9745;");
+            checkbox.attr('title', "select all checkboxes below")
+                .bsTooltip('fixTitle')
+                .data('bs.tooltip')
+                .$tip.find('.tooltip-inner')
+                .text("select all checkboxes below");
+        }
+    }
+
     function onLegendClearClick(ev) { 
         /* unselect all checkboxes in the legend and clear the selection */ 
-        renderer.selectClear();
-        renderer.drawDots();
-
-        var cboxes = document.getElementsByClassName("tpLegendCheckbox");
-        for (var i=0; i < cboxes.length; i++) {
-            cboxes[i].checked = false;
+        if (gLegend.selectionDirection == "all") {
+            onSelectAllClick()
+        } else {
+            onSelectNoneClick();
         }
         ev.stopPropagation();
     }
@@ -5217,6 +5288,7 @@ var cellbrowser = function() {
             renderer.unselectByColor(valIdx);
         renderer.drawDots();
         ev.stopPropagation();
+        $(this).blur();
     }
 
     function buildMinMaxPart(htmls) {
diff --git a/src/cbPyLib/cellbrowser/cbWeb/js/maxPlot.js b/src/cbPyLib/cellbrowser/cbWeb/js/maxPlot.js
index b84a04db..1bfb90f1 100644
--- a/src/cbPyLib/cellbrowser/cbWeb/js/maxPlot.js
+++ b/src/cbPyLib/cellbrowser/cbWeb/js/maxPlot.js
@@ -174,7 +174,7 @@ function MaxPlot(div, top, left, width, height, args) {
         self.col.pal = null;        // list of six-digit hex codes 
         self.col.arr = null;        // length is coords.px/2, one byte per cell = index into self.col.pal
 
-        self.selCells   = [];  // IDs of cells that are selected (drawn in black)
+        self.selCells = new Set();  // IDs of cells that are selected (drawn in black)
 
         self.doDrawLabels = true;  // should cluster labels be drawn?
         self.initPort(args);
@@ -652,13 +652,12 @@ function MaxPlot(div, top, left, width, height, args) {
        // draw the selection as black rectangles
        ctx.globalAlpha = 0.7;
        ctx.fillStyle="black";
-       for (i = 0; i < selCells.length; i++) {
-           var cellId = selCells[i];
+        selCells.forEach(function(cellId) {
            let pxX = pxCoords[2*cellId];
            let pxY = pxCoords[2*cellId+1];
            ctx.fillRect(pxX-radius, pxY-radius, dblSize, dblSize);
            count += 1;
-       }
+        })
        console.log(count+" rectangles drawn (including selection)");
        ctx.restore();
        return count;
@@ -907,18 +906,17 @@ function MaxPlot(div, top, left, width, height, args) {
        
        // overdraw the selection as solid black circle outlines
        ctx.globalAlpha = 0.7;
-       for (i = 0; i < selCells.length; i++) {
-           var cellId = selCells[i];
+        selCells.forEach(function(cellId) {
            let pxX = pxCoords[2*cellId];
            let pxY = pxCoords[2*cellId+1];
            if (isHidden(pxX, pxY))
-               continue;
+                return;
            // make sure that old leftover overlapping black circles don't shine through
            let col = coordColors[cellId];
            ctx.drawImage(off, col * tileWidth, 0, tileWidth, tileHeight, pxX - radius -1, pxY - radius-1, tileWidth, tileHeight);
 
            ctx.drawImage(off, selImgId * tileWidth, 0, tileWidth, tileHeight, pxX - radius -1, pxY - radius-1, tileWidth, tileHeight);
-       }
+        })
 
        console.log(count +" circles drawn");
        ctx.restore();
@@ -1020,17 +1018,16 @@ function MaxPlot(div, top, left, width, height, args) {
        }
        
        // overdraw the selection as black pixels
-       for (i = 0; i < selCells.length; i++) {
-           var cellId = selCells[i];
+        selCells.forEach(function(cellId) {
            let pxX = pxCoords[2*cellId];
            let pxY = pxCoords[2*cellId+1];
            if (isHidden(pxX, pxY))
-               continue;
+                return;
            let p = 4 * (pxY*width+pxX); // pointer to red value of pixel at x,y
            cData[p] = 0; 
            cData[p+1] = 0;
            cData[p+2] = 0;
-       }
+        })
 
        self.ctx.putImageData(canvasData, 0, 0);
        return count;
@@ -1493,30 +1490,29 @@ function MaxPlot(div, top, left, width, height, args) {
     
     this.selectClear = function() {
         /* clear selection */
-        self.selCells.length = 0;
+        self.selCells.clear();
         setStatus("");
         if (self.onSelChange!==null)
-            self.onSelChange([]);
+            self.onSelChange(self.selCells);
     };
 
     this.selectSet = function(cellIds) {
         /* set selection to an array of integer cellIds */
-        self.selCells.length = 0;
+        self.selCells.clear();
         //self.selCells.push(...cellIds); // "extend" = array spread syntax, https://davidwalsh.name/spread-operator
         let selCells = self.selCells;
         for (let i=0; i<cellIds.length; i++)
-            selCells.push(cellIds[i]);
+            selCells.add(cellIds[i]);
         self._selUpdate();
     };
 
     this.selectAdd = function(cellIdx) {
         /* add a single cell to the selection. If it already exists, remove it. */
         console.time("selectAdd");
-        var foundIdx = self.selCells.indexOf(cellIdx);
-        if (foundIdx===-1)
-            self.selCells.push(cellIdx);
+        if (self.selCells.has(cellIdx))
+            self.selCells.delete(cellIdx);
         else
-            self.selCells.splice(foundIdx, 1);
+            self.selCells.add(cellIdx);
         console.time("selectAdd");
         self._selUpdate();
     };
@@ -1530,7 +1526,7 @@ function MaxPlot(div, top, left, width, height, args) {
             var pxY = pxCoords[2*i+1];
             if (isHidden(pxX, pxY))
                continue;
-            selCells.push(i); // XX: DUPLICATES?
+            selCells.add(i);
         }
         self.selCells = selCells;
         self._selUpdate();
@@ -1540,12 +1536,15 @@ function MaxPlot(div, top, left, width, height, args) {
         /* add all cells with a given color to the selection */
         var colArr = self.col.arr;
         var selCells = self.selCells;
+        var cnt = 0;
         for (var i = 0; i < colArr.length; i++) {
-            if (colArr[i]===colIdx)
-                selCells.push(i); // XX  duplicates ?
+            if (colArr[i]===colIdx) {
+                selCells.add(i);
+                cnt++;
+            }
         }
         self.selCells = selCells;
-        console.log(self.selCells.length+" cells appended to selection, by color");
+        console.log(cnt + " cells appended to selection, by color");
         self._selUpdate();
     };
 
@@ -1553,24 +1552,16 @@ function MaxPlot(div, top, left, width, height, args) {
         /* remove all cells with a given color from the selection */
         var colArr = self.col.arr;
         var selCells = self.selCells;
-
-        // make set of all cells to remove
-        var removeCells = new Set();
+        var cnt = 0;
         for (var i = 0; i < colArr.length; i++) {
-            if (colArr[i]===colIdx)
-                removeCells.add(i);
-        }
-
-        // copy selection, skipping cells that should be removed
-        var newSel = [];
-        for (var i = 0; i < selCells.length; i++) {
-            var selId = selCells[i];
-            if (!removeCells.has(selId))
-                newSel.push(selId); // XX  duplicates ?
+            if (colArr[i]===colIdx) {
+                selCells.delete(i);
+                cnt++;
+            }
         }
 
-        self.selCells = newSel;
-        console.log(removeCells.length+" cells removed from selection, by color");
+        self.selCells = selCells;
+        console.log(cnt + " cells removed from selection, by color");
         self._selUpdate();
     };
 
@@ -1590,7 +1581,7 @@ function MaxPlot(div, top, left, width, height, args) {
             if (isHidden(pxX, pxY))
                continue;
             if ((minX <= pxX) && (pxX <= maxX) && (minY <= pxY) && (pxY <= maxY)) {
-                self.selCells.push(i); // XX  duplicates?
+                self.selCells.add(i);
             }
 
         }
@@ -1600,22 +1591,21 @@ function MaxPlot(div, top, left, width, height, args) {
 
     this.getSelection = function() {
         /* return selected cells as a list of ints */
-        return self.selCells;
+        var cellIds = [];
+        self.selCells.forEach(function(x) {cellIds.push(x)});
+        return cellIds;
     };
     
     this.selectInvert = function() {
         /* invert selection */
         var selCells = self.selCells;
-        var selCellsObj = new Set();
-        for (var i = 0; i < selCells.length; i++) { // IE11 doesn't have array init constructor
-                selCellsObj.add(selCells[i]);
-        }
-
-        selCells.length = 0; // keep the same object
         var cellCount = self.getCount();
         for (let i = 0; i < cellCount; i++) {
-            if (! selCellsObj.has(i))
-                selCells.push(i);
+            if (selCells.has(i)) {
+                selCells.delete(i);
+            } else {
+                selCells.add(i);
+            }
         }
         self.selCells = selCells;
         self._selUpdate();
@@ -1623,14 +1613,14 @@ function MaxPlot(div, top, left, width, height, args) {
     
     this.getCount = function() {
         /* return maximum number of cells in dataset, may include hidden cells, see isHidden() */
-        return self.coords.orig.length;
+        return self.coords.orig.length / 2;
     };
     
     // END SELECTION METHODS (could be an object?)
 
     this._selUpdate = function() {
         /* called after the selection has been updated, calls the onSelChange callback */
-        setStatus(self.selCells.length+" "+self.gSampleDescription+"s selected");
+        setStatus(self.selCells.size + " " + self.gSampleDescription + "s selected");
         if (self.onSelChange!==null)
             self.onSelChange(self.selCells);
     }
@@ -1907,8 +1897,9 @@ function MaxPlot(div, top, left, width, height, args) {
             if (self.lastClick!==undefined && x2===self.lastClick[0] && y2===self.lastClick[1]) {
                 self.zoomBy(1.33);
                 self.lastClick = [-1,-1];
+            } else {
+                self.lastClick = [x2, y2];
             }
-            self.lastClick = [x2, y2];
 
             var labelInfo = self.labelAt(x2, y2);
             if (labelInfo!==null && self.doDrawLabels)
@@ -1917,7 +1908,10 @@ function MaxPlot(div, top, left, width, height, args) {
                 var clickedCellIds = self.cellsAt(x2, y2);
                 // click on a cell -> update selection and redraw
                 if (clickedCellIds!==null && self.onCellClick!==null) {
-                    self.selCells = clickedCellIds;
+                    self.selectClear();
+                    for (var i = 0; i < clickedCellIds.length; i++) {
+                        self.selCells.add(clickedCellIds[i]);
+                    }
                     self.drawDots();
                     self.onCellClick(clickedCellIds, ev);
 
diff --git a/src/cbPyLib/cellbrowser/cellbrowser.py b/src/cbPyLib/cellbrowser/cellbrowser.py
index 267259e1..0b173b20 100755
--- a/src/cbPyLib/cellbrowser/cellbrowser.py
+++ b/src/cbPyLib/cellbrowser/cellbrowser.py
@@ -17,6 +17,7 @@
 from collections import namedtuple, OrderedDict
 from os.path import join, basename, dirname, isfile, isdir, relpath, abspath, getsize, getmtime, expanduser
 from time import gmtime, strftime
+import csv
 
 try:
     # python3
@@ -2462,10 +2463,10 @@ def parseMarkerTable(filename, geneToSym):
     otherHeaders = headers[otherStart:otherEnd]
     logging.debug("Other headers: %s" % otherHeaders)
 
+    reader = csv.reader(ifh, delimiter=sep, quotechar='"')
     data = defaultdict(list)
     otherColumns = defaultdict(list)
-    for line in ifh:
-        row = line.rstrip("\r\n").split(sep)
+    for row in reader:
         clusterName = row[clusterIdx]
         geneId = row[geneIdx]
         scoreVal = float(row[scoreIdx])
@@ -4165,8 +4166,9 @@ def findRoot(inDir=None):
 def resolveOutDir(outDir):
     """ user can define mapping e.g. {"alpha" : "/usr/local/apache/htdocs-cells"} in ~/.cellbrowser.conf """
     confDirs = getConfig("outDirs")
-    if outDir in confDirs:
-        outDir = confDirs[outDir]
+    if confDirs:
+        if outDir in confDirs:
+            outDir = confDirs[outDir]
     return outDir
 
 def build(confFnames, outDir, port=None, doDebug=False, devMode=False, redo=None):