diff --git a/js/collate.js b/js/collate.js
deleted file mode 100644
index f45c4f7..0000000
--- a/js/collate.js
+++ /dev/null
@@ -1,81 +0,0 @@
-var ipc = require('electron').ipcRenderer;
-var run = document.getElementById('run');
-var indir = document.getElementById('indir');
-var outdir = document.getElementById('outdir');
-var loadbar = document.getElementById('loadbar');
-var loadmessage = document.getElementById('loadmessage');
-var back = document.getElementById('back');
-var regions = document.getElementById('regions');
-
-function checkNumber(value, message) {
-    var str = value.toString();
-    if(!str.match(/^-?\d*\.?\d*$/)) {
-        alert(`${message}`);
-        return false;
-    }
-    return true;
-}
-
-run.addEventListener('click', function(){
-    if (indir && outdir && indir.value && outdir.value) {
-        run.classList.add('disabled');
-        back.classList.remove('btn-warning');
-        back.classList.add('btn-danger')
-        back.innerHTML = "Cancel";
-        run.innerHTML = "<i class='fas fa-spinner fa-spin'></i>";
-        ipc.send('runCollate', [indir.value, outdir.value, regions.innerText]);
-        loadmessage.innerHTML = "Intializing...";
-    }
-});
-
-back.addEventListener('click', function (event){
-    if (back.classList.contains('btn-danger')){
-        event.preventDefault();
-        ipc.send('killDetect', []);
-        back.classList.add('btn-warning');
-        back.classList.remove('btn-danger')
-        back.innerHTML = "Back";
-        run.innerHTML = "Run";
-        run.classList.remove('disabled');
-        loadmessage.innerHTML = "";
-        loadbar.style.width = "0";
-    }
-});
-
-ipc.on('collateResult', function(event, response){
-    back.classList.add('btn-warning');
-    back.classList.remove('btn-danger')
-    back.innerHTML = "Back";
-    run.innerHTML = "Run";
-    run.classList.remove('disabled');
-    loadmessage.innerHTML = "";
-    loadbar.style.width = "0";
-});
-
-ipc.once('detectError', function(event, response){
-    run.innerHTML = "Run";
-    run.classList.remove('disabled');
-});
-
-ipc.on('updateLoad', function (event, response) {
-    loadbar.style.width = String(response[0]) + "%";
-    loadmessage.innerHTML = response[1];
-});
-
-indir.addEventListener('click', function(){
-    ipc.once('returnPath', function(event, response){
-        if (response[1] == 'indir') {
-            indir.value = response[0];
-        }
-    })
-    ipc.send('openFileDialog', 'indir');
-});
-
-outdir.addEventListener('click', function(){
-    ipc.once('returnPath', function(event, response){
-        if (response[1] == 'outdir') {
-            outdir.value = response[0];
-        }
-    })
-    ipc.send('openDialog', 'outdir');
-});
\ No newline at end of file
diff --git a/js/count.js b/js/count.js
deleted file mode 100644
index dd2108c..0000000
--- a/js/count.js
+++ /dev/null
@@ -1,86 +0,0 @@
-var ipc = require('electron').ipcRenderer;
-var run = document.getElementById('run');
-var preddir = document.getElementById('preddir');
-var annodir = document.getElementById('annodir');
-var outdir = document.getElementById('outdir');
-var loadbar = document.getElementById('loadbar');
-var loadmessage = document.getElementById('loadmessage');
-var layerinfo = document.getElementById('layerinfo');
-var back = document.getElementById('back');
-
-run.addEventListener('click', function(){
-    if (preddir && annodir && outdir && preddir.value && annodir.value && outdir.value) {
-        run.classList.add('disabled');
-        back.classList.remove('btn-warning');
-        back.classList.add('btn-danger')
-        back.innerHTML = "Cancel";
-        run.innerHTML = "<i class='fas fa-spinner fa-spin'></i>";
-
-        var should_layer = layerinfo.checked;
-
-        ipc.send('runCount', [preddir.value, annodir.value, outdir.value, should_layer]);
-    }
-});
-
-back.addEventListener('click', function (event){
-    if (back.classList.contains('btn-danger')){
-        event.preventDefault();
-        ipc.send('killCount', []);
-        back.classList.add('btn-warning');
-        back.classList.remove('btn-danger')
-        back.innerHTML = "Back";
-        run.innerHTML = "Run";
-        run.classList.remove('disabled');
-        loadmessage.innerHTML = "";
-        loadbar.style.width = "0";
-    }
-});
-
-ipc.on('countResult', function(event, response){
-    run.innerHTML = "Run";
-    run.classList.remove('disabled');
-    back.classList.add('btn-warning');
-    back.classList.remove('btn-danger')
-    back.innerHTML = "Back";
-    run.innerHTML = "Run";
-    run.classList.remove('disabled');
-    loadmessage.innerHTML = "";
-    loadbar.style.width = "0";
-});
-
-ipc.on('countError', function(event, response){
-    run.innerHTML = "Run";
-    run.classList.remove('disabled');
-});
-
-ipc.on('updateLoad', function (event, response) {
-    loadbar.style.width = String(response[0]) + "%";
-    loadmessage.innerHTML = response[1];
-});
-
-preddir.addEventListener('click', function(){
-    ipc.once('returnPath', function(event, response){
-        if (response[1] == 'preddir') {
-            preddir.value = response[0];
-        }
-    })
-    ipc.send('openDialog', 'preddir');
-});
-
-annodir.addEventListener('click', function(){
-    ipc.once('returnPath', function(event, response){
-        if (response[1] == 'annodir') {
-            annodir.value = response[0];
-        }
-    })
-    ipc.send('openDialog', 'annodir');
-});
-
-outdir.addEventListener('click', function(){
-    ipc.once('returnPath', function(event, response){
-        if (response[1] == 'outdir') {
-            outdir.value = response[0];
-        }
-    })
-    ipc.send('openDialog', 'outdir');
-});
\ No newline at end of file
diff --git a/js/detect.js b/js/detect.js
deleted file mode 100644
index 3b31e11..0000000
--- a/js/detect.js
+++ /dev/null
@@ -1,125 +0,0 @@
-var ipc = require("electron").ipcRenderer;
-var run = document.getElementById("run");
-var indir = document.getElementById("indir");
-var outdir = document.getElementById("outdir");
-var loadbar = document.getElementById("loadbar");
-var tile = document.getElementById("tile");
-var confidence = document.getElementById("confidence");
-var model = document.getElementById("model");
-var loadmessage = document.getElementById("loadmessage");
-var back = document.getElementById("back");
-var advance = document.getElementById("advance");
-var arrow = document.getElementById("arrow");
-var multichannel = document.getElementById("multichannel");
-
-advance.addEventListener("click", function () {
-	arrow.classList.toggle("down");
-});
-
-function checkNumber(value, message) {
-	var str = value.toString();
-	if (!str.match(/^-?\d*\.?\d*$/)) {
-		alert(`${message}`);
-		return false;
-	}
-	return true;
-}
-
-run.addEventListener("click", function () {
-	var c = 0.5;
-	var t = 640;
-	var m = "";
-	var mc = false;
-
-	if (indir && outdir && indir.value && outdir.value) {
-		if (confidence.value && confidence.value < 1 && confidence.value > 0) {
-			c = checkNumber(
-				confidence.value,
-				"Confidence should be a float between 0-1, using default."
-			)
-				? confidence.value
-				: 0.5;
-		}
-		if (tile.value && tile.value > 0) {
-			t = checkNumber(tile.value, "Tile should be an integer, using default.")
-				? tile.value
-				: 640;
-		}
-		if (model.value) {
-			m = model.value;
-		}
-		if (multichannel.checked) {
-			mc = true;
-		}
-
-		run.classList.add("disabled");
-		back.classList.remove("btn-warning");
-		back.classList.add("btn-danger");
-		back.innerHTML = "Cancel";
-		run.innerHTML = "<i class='fas fa-spinner fa-spin'></i>";
-		loadmessage.innerHTML = "Intializing...";
-
-		ipc.send("runDetection", [indir.value, outdir.value, c, t, m, mc]);
-	}
-});
-
-back.addEventListener("click", function (event) {
-	if (back.classList.contains("btn-danger")) {
-		event.preventDefault();
-		ipc.send("killDetect", []);
-		back.classList.add("btn-warning");
-		back.classList.remove("btn-danger");
-		back.innerHTML = "Back";
-		run.innerHTML = "Run";
-		run.classList.remove("disabled");
-		loadmessage.innerHTML = "";
-		loadbar.style.width = "0";
-	}
-});
-
-ipc.on("detectResult", function (event, response) {
-	back.classList.add("btn-warning");
-	back.classList.remove("btn-danger");
-	back.innerHTML = "Back";
-	run.innerHTML = "Run";
-	run.classList.remove("disabled");
-	loadmessage.innerHTML = "";
-	loadbar.style.width = "0";
-});
-
-ipc.on("detectError", function (event, response) {
-	run.innerHTML = "Run";
-	run.classList.remove("disabled");
-});
-
-ipc.on("updateLoad", function (event, response) {
-	loadbar.style.width = String(response[0]) + "%";
-	loadmessage.innerHTML = response[1];
-});
-
-indir.addEventListener("click", function () {
-	ipc.once("returnPath", function (event, response) {
-		if (response[1] == "indir") {
-			indir.value = response[0];
-		}
-	});
-	ipc.send("openDialog", "indir");
-});
-
-outdir.addEventListener("click", function () {
-	ipc.once("returnPath", function (event, response) {
-		if (response[1] == "outdir") {
-			outdir.value = response[0];
-		}
-	});
-	ipc.send("openDialog", "outdir");
-});
-
-model.addEventListener("click", function () {
-	ipc.once("returnPath", function (event, response) {
-		if (response[1] == "model") {
-			model.value = response[0];
-		}
-	});
-	ipc.send("openFileDialog", "model");
-});
diff --git a/js/intensity.js b/js/intensity.js
deleted file mode 100644
index 56c824e..0000000
--- a/js/intensity.js
+++ /dev/null
@@ -1,99 +0,0 @@
-var ipc = require("electron").ipcRenderer;
-var run = document.getElementById("run");
-var indir = document.getElementById("indir");
-var annodir = document.getElementById("annodir");
-var outdir = document.getElementById("outdir");
-var loadbar = document.getElementById("loadbar");
-var loadmessage = document.getElementById("loadmessage");
-var back = document.getElementById("back");
-var whole = document.getElementById("whole");
-var half = document.getElementById("half");
-var alignmentMethod = "True";
-var methods = document.querySelector("#methods");
-
-whole.addEventListener("click", function () {
-	methods.textContent = "Whole Slice";
-	alignmentMethod = "True";
-	console.log(alignmentMethod);
-});
-
-half.addEventListener("click", function () {
-	methods.textContent = "Hemisphere Only";
-	alignmentMethod = "False";
-	console.log(alignmentMethod);
-});
-
-run.addEventListener("click", function () {
-	if (indir && outdir && indir.value && outdir.value && annodir && annodir.value) {
-
-		run.classList.add("disabled");
-		back.classList.remove("btn-warning");
-		back.classList.add("btn-danger");
-		back.innerHTML = "Cancel";
-		run.innerHTML = "<i class='fas fa-spinner fa-spin'></i>";
-		ipc.send("runIntensity", [indir.value, outdir.value, annodir.value, alignmentMethod]);
-	}
-});
-
-back.addEventListener("click", function (event) {
-	if (back.classList.contains("btn-danger")) {
-		event.preventDefault();
-		ipc.send("killIntensity", []);
-		back.classList.add("btn-warning");
-		back.classList.remove("btn-danger");
-		back.innerHTML = "Back";
-		run.innerHTML = "Run";
-		run.classList.remove("disabled");
-		loadmessage.innerHTML = "";
-		loadbar.style.width = "0";
-	}
-});
-
-ipc.on("intensityResult", function (event, response) {
-	run.innerHTML = "Run";
-	run.classList.remove("disabled");
-	back.classList.add("btn-warning");
-	back.classList.remove("btn-danger");
-	back.innerHTML = "Back";
-	run.innerHTML = "Run";
-	run.classList.remove("disabled");
-	loadmessage.innerHTML = "";
-	loadbar.style.width = "0";
-});
-
-ipc.on("intensityError", function (event, response) {
-	run.innerHTML = "Run";
-	run.classList.remove("disabled");
-});
-
-ipc.on("updateLoad", function (event, response) {
-	loadbar.style.width = String(response[0]) + "%";
-	loadmessage.innerHTML = response[1];
-});
-
-indir.addEventListener("click", function () {
-	ipc.once("returnPath", function (event, response) {
-		if (response[1] == "indir") {
-			indir.value = response[0];
-		}
-	});
-	ipc.send("openDialog", "indir");
-});
-
-outdir.addEventListener("click", function () {
-	ipc.once("returnPath", function (event, response) {
-		if (response[1] == "outdir") {
-			outdir.value = response[0];
-		}
-	});
-	ipc.send("openDialog", "outdir");
-});
-
-annodir.addEventListener("click", function () {
-	ipc.once("returnPath", function (event, response) {
-		if (response[1] == "annodir") {
-			annodir.value = response[0];
-		}
-	});
-	ipc.send("openDialog", "annodir");
-});
\ No newline at end of file
diff --git a/main.js b/main.js
index 8cec154..3d058ab 100644
--- a/main.js
+++ b/main.js
@@ -522,13 +522,13 @@ function setupMambaEnv(win) {
         miniforgePath = path.join(homeDir, 'miniforge');
         mambaPath = path.join(miniforgePath, 'condabin', 'mamba');
         pipPath = path.join(miniforgePath, 'Scripts', 'pip'); // Adjust for Windows if necessary
-        imswitchPath = path.join(miniforgePath, 'site-packages', 'imswitch')
+        imswitchPath = path.join(miniforgePath, 'Lib', 'site-packages', 'imswitch')
     }
     else {
         miniforgePath = path.join(homeDir, 'miniforge');
         mambaPath = path.join(miniforgePath, 'bin', 'mamba');
         pipPath = path.join(miniforgePath, 'bin', 'pip');
-        imswitchPath = path.join(miniforgePath, 'site-packages', 'imswitch')
+        imswitchPath = path.join(miniforgePath,  'site-packages', 'imswitch')
     }
     /*
     Install UC2-REST and ImSwitch from github master
@@ -686,7 +686,7 @@ function setupMambaEnv(win) {
                 }
             }
         });
-        checkForUpdates();
+        //checkForUpdates();
         win.webContents.once("did-finish-load", () => {
             // Make a directory to house enviornment, settings, etc.yarn
             checkLocalDir();