Batch Median Noise Reduction

@Seta666 

Try the following code and let me know how it goes. It will combine files into sets of 4 and merge into a smart object stack with median blend mode.  A new directory will be created within the input folder where the files are saved.  File names are based off either the 4th, 8th etc file name in each set of 4 – or it is easily modified to use the 1st, 5th name etc.

Filenames are expected to be in correct alpha/numeric sorting order.

/* 

Stack Sets of 4 Images with Median Blend.jsx

Stephen Marsh - 17th April 2021

This script is based around alpha/numeric sorting files

Batch Median Noise Reduction
https://community.adobe.com/t5/photoshop/batch-median-noise-reduction/m-p/11960956#M529922

*/

#target photoshop

if (app.documents.length === 0) {

    try {

        // Save and disable dialogs
        var restoreDialogMode = app.displayDialogs;
        app.displayDialogs = DialogModes.NO;

        batchSetProcessing();

        function batchSetProcessing() {

            // Select the input folder
            inputFolder = Folder.selectDialog('Please select the folder with files to process');
            if (inputFolder === null) return;

            // Create the output sub-directory
            var outputFolder = Folder(decodeURI(inputFolder + '/Output Sets Folder'));
            if (!outputFolder.exists) outputFolder.create();

            // Limit the file format input
            var fileList = inputFolder.getFiles(/\.(tif|tiff)$/i);

            // Force alpha-numeric list sort
            // Use .reverse() for the first filename in the merged file
            // Remove .reverse() for the last filename in the merged file
            fileList.sort().reverse();

            // Images per set
            var setQty = 4;

            // Validate the input count vs. output count
            var inputCount = fileList.length;
            // Thanks to Kukurykus for the advice to test using % modulus
            var cancelScript = !(inputCount % setQty);
            alert(inputCount + ' input files stacked into sets of ' + setQty + ' will produce ' + inputCount / setQty + ' file sets.');
            // Test if false, then terminate the script
            if (cancelScript === false) {
                alert('Script cancelled as the quantity of input files are not evenly divisible by the set quantity.');
                return;
            }

            // Loop through and open the file sets
            while (fileList.length) {
                // Sets of N files
                for (var a = 0; a < setQty; a++) {
                    try {
                        app.open(fileList.pop());
                    } catch (e) { }
                }

                processOpenImages();

            }

            // End of script notification
            var outputList = outputFolder.getFiles(/\.(tif|tiff)$/i);
            alert('Script completed!' + '\n' + outputList.length + ' combined files saved to:' + '\n' + outputFolder.fsName);

            // Restore saved dialogs
            app.displayDialogs = restoreDialogMode;

            function processOpenImages() {

                try {

                    app.activeDocument = documents[0];
                    docNameToLayerName();

                    // Combine open docs to base doc
                    while (app.documents.length) {
                        app.activeDocument = documents[1];
                        docNameToLayerName();
                        app.activeDocument.activeLayer.duplicate(documents[0]);
                        app.activeDocument.close(SaveOptions.DONOTSAVECHANGES);
                    }

                    app.activeDocument.flatten();

                    function docNameToLayerName() {
                        var layerName = app.activeDocument.name.replace(/\.[^\.]+$/, '');
                        app.activeDocument.activeLayer.name = layerName;
                    }

                } catch (e) { }

                // Select all layers
                app.runMenuItem(stringIDToTypeID("selectAllLayers"));

                // Create a smart object from all selected layers
                makeSO();

                // Smart object median stack blend mode
                makeMedian();

                // Save name+suffix & save path
                var Name = app.activeDocument.name.replace(/\.[^\.]+$/, '');
                var saveFile = File(outputFolder + '/' + Name + '_MedianBlend' + '.tif');

                // Call the save function
                saveTIFF(saveFile);

                // Close all open files without saving
                while (app.documents.length) {
                    app.activeDocument.close(SaveOptions.DONOTSAVECHANGES);
                }

                // Functions

                function makeSO() {
                    var idnewPlacedLayer = stringIDToTypeID("newPlacedLayer");
                    executeAction(idnewPlacedLayer, undefined, DialogModes.NO);
                }

                function makeMedian() {
                    var idapplyImageStackPluginRenderer = stringIDToTypeID("applyImageStackPluginRenderer");
                    var desc6 = new ActionDescriptor();
                    var idimageStackPlugin = stringIDToTypeID("imageStackPlugin");
                    var idmedn = charIDToTypeID("medn");
                    desc6.putClass(idimageStackPlugin, idmedn);
                    var idNm = charIDToTypeID("Nm  ");
                    desc6.putString(idNm, """Median""");
                    executeAction(idapplyImageStackPluginRenderer, desc6, DialogModes.NO);
                }

                function saveTIFF(saveFile) {
                    tiffSaveOptions = new TiffSaveOptions();
                    tiffSaveOptions.embedColorProfile = true;
                    tiffSaveOptions.byteOrder = ByteOrder.IBM;
                    tiffSaveOptions.transparency = true;
                    // Change .layers to true to preserve layers
                    tiffSaveOptions.layers = false;
                    tiffSaveOptions.layerCompression = LayerCompression.ZIP;
                    tiffSaveOptions.interleaveChannels = true;
                    tiffSaveOptions.alphaChannels = true;
                    tiffSaveOptions.annotations = true;
                    tiffSaveOptions.spotColors = true;
                    tiffSaveOptions.saveImagePyramid = false;
                    // Image compression = NONE | JPEG | TIFFLZW | TIFFZIP
                    tiffSaveOptions.imageCompression = TIFFEncoding.TIFFLZW;
                    // Save as
                    app.activeDocument.saveAs(saveFile, tiffSaveOptions, true, Extension.LOWERCASE);
                }
            }
        }

    } catch (e) {
        // Restore saved dialogs
        app.displayDialogs = restoreDialogMode;
    }

} else {
    alert('Please close all open documents before running this script!');
}

So, I'm curious how the end video looked by combining the layers in this way? No odd artifacts from ghosting images?

Try this script. It will pull the files from a folder on your desktop called "source," but you can change the folder by editing the path in the code. It will save to a subfolder, called done, in the same folder. It will append the files with "median" so files don't get over written. It will also save the files as jpgs, and only open jpgs. You can change the file type by changing the extension in the line: 

var mask = '*.jpg'

#target photoshop
var srcFolder = new Folder('~/desktop/source/');
var doneFolder = new Folder(srcFolder + '/done/');
if(!doneFolder.exists){doneFolder.create()};

var jpgOptions = new JPEGSaveOptions();
jpgOptions.quality = 8
var mask = '*.jpg'
var fList = srcFolder.getFiles (mask);

for(var i=0;i<fList.length;i++){
    try{
        open(fList[i])
        }
    catch(e){};
    try{
        open(fList[i -1])
        }
    catch(e){};
    try{
        open(fList[i +1])
        }
    catch(e){};
    
    var base = activeDocument = app.documents[0];
    base.flatten();
    base.layers[0].isBackgroundLayer = false;
    var docNum = app.documents.length;
    for(var j=1;j<docNum;j++){
        var nextDoc = activeDocument = app.documents[1];
        nextDoc.flatten();
        nextDoc.activeLayer.duplicate (base.layers[0], ElementPlacement.PLACEBEFORE);
        nextDoc.close(SaveOptions.DONOTSAVECHANGES);
        }
    
    base.layers[base.layers.length -1].isBackgroundLayer = false;
    selectAllLayers ();
    makeSO ();
    makeMedian ();
    base.flatten();
    var fName = base.name.split('.')[0];
    base.saveAs (new File(doneFolder + '/Median-' + fName + '.jpg'), jpgOptions);
    base.close(SaveOptions.DONOTSAVECHANGES);
    };//end loop

function selectAllLayers(){
    var idselectAllLayers = stringIDToTypeID( "selectAllLayers" );
        var desc3 = new ActionDescriptor();
        var idnull = charIDToTypeID( "null" );
            var ref1 = new ActionReference();
            var idLyr = charIDToTypeID( "Lyr " );
            var idOrdn = charIDToTypeID( "Ordn" );
            var idTrgt = charIDToTypeID( "Trgt" );
            ref1.putEnumerated( idLyr, idOrdn, idTrgt );
        desc3.putReference( idnull, ref1 );
    executeAction( idselectAllLayers, desc3, DialogModes.NO );
    }

function makeSO(){
    var idnewPlacedLayer = stringIDToTypeID( "newPlacedLayer" );
    executeAction( idnewPlacedLayer, undefined, DialogModes.NO );    
    }

function makeMedian(){
    var idapplyImageStackPluginRenderer = stringIDToTypeID( "applyImageStackPluginRenderer" );
        var desc6 = new ActionDescriptor();
        var idimageStackPlugin = stringIDToTypeID( "imageStackPlugin" );
        var idmedn = charIDToTypeID( "medn" );
        desc6.putClass( idimageStackPlugin, idmedn );
        var idNm = charIDToTypeID( "Nm  " );
        desc6.putString( idNm, """Median""" );
    executeAction( idapplyImageStackPluginRenderer, desc6, DialogModes.NO );    
    }

"I didn't find a way to open more than one image automatically..."

File > Scripts > Load Files into Stack command can open multiple files and position them one above another in the Layers panel if I understand what you want to ask.

Did you shoot three shots for each frame, or are you wanting to combing the two frames before and after the selected frame?