Merge pull request #3 from FrancisCrickInstitute/main

Merge content from Crick workshop

Pages/Installation-Instructions.md

@@ -4,6 +4,10 @@ Please read the following instructions carefully to prepare for the workshop. Co
 * For issues with FIJI, contact Dave ([email protected])
 * For conda issues, contact Stefania ([email protected])
 
+## Download Demo Data
+
+Download the workshop data by clicking on the link to the ZIP archive at the top of this page.
+
 ## Installing FIJI
 
 1. Download FIJI from [here](https://fiji.sc/).

README.md

@@ -21,9 +21,13 @@ In this workshop, we will bridge the gap between advanced microscopy data genera
 1. Please remember to bring your laptop (and charger).
 2. Please install the required software before the workshop - follow the installation instructions on [this page](Pages/Installation-Instructions.md).
 3. Download the workshop data by clicking on the link to the ZIP archive at the top of this page.
-4. You will be assigned to a specific group, with whom you will be sitting - your group number will be displayed [here](Pages/Groups.md).
+4. You will be assigned to a specific group, with whom you will be sitting - your group number will be displayed in the training room.
 5. **PLEASE CONTACT US BEFORE THE WORKSHOP IF YOU ENCOUNTER ANY DIFFICULTIES WITH ANY OF THE ABOVE.**
 
+# Slides
+
+All the slides for the workshop are on Google and accesible [here](https://drive.google.com/drive/folders/1nTeM1MHu74hpmGDSvYeqU-ftX8ANHqI_?usp=sharing).
+
 # Program
 
 **Please note that all catering, as well as attendance of the social on the evening of the 21st, is covered by your registration fee.**
@@ -118,7 +122,7 @@ In this workshop, we will bridge the gap between advanced microscopy data genera
 		<tr>
 			<td>18:00 - ?</td>
 			<td>Evening Social</td>
-			<td>TBC</td>
+			<td>The Lighterman, 3 Granary Square, N1C 4BH</td>
 		</tr>
 		<tr>
 			<th colspan=3>Tuesday, October 22nd 2024</th>

Scripts/FIJI/Counting.ijm

@@ -10,13 +10,18 @@
  */
 
 // Specify the input directory
-inputDir = "C:/Users/davej/GitRepos/Pages/introduction-to-image-analysis/Data/idr0028"
+inputDir = getDirectory("Select Input Directory");
 
 // Get the list of files in the input directory
 images = getFileList(inputDir);
 
+print("\\Clear");
+print("Found " + images.length + " files in " + inputDir);
+print("0% of images processed.");
+
 // Iterate over all files
 for (i = 0; i < images.length; i++) {
+	print("\\Update:" + (100.0 * i / images.length) + "% of images processed.");
 	// Open each image with Bio-Formats (www.openmicroscopy.org/bio-formats) to ensure correct reading of metadata
 	run("Bio-Formats Importer", "open=[" + inputDir + File.separator() + images[i] + "] autoscale color_mode=Composite rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
 	// Split the image into constituent channels - this could also be done in the step above via Bio-Formats
@@ -34,3 +39,4 @@ for (i = 0; i < images.length; i++) {
 	// Close all open images
 	close("*");
 }
+print("\\Update:100% of images processed.");

Scripts/Jupyter/napari_for_visualisation.ipynb

@@ -56,7 +56,7 @@
     "\n",
     "import napari\n",
     "\n",
-    "from aicsimageio import AICSImage"
+    "from bioio import BioImage"
    ]
   },
   {
@@ -150,10 +150,10 @@
    "outputs": [],
    "source": [
     "viewer = napari.Viewer()\n",
-    "viewer.add_image(im_all[0,], name='nuclei', colormap='cyan')\n",
-    "viewer.add_image(im_all[1,], name='tubulin', colormap='magenta')\n",
-    "viewer.add_image(im_all[2,], name='actin', colormap='green')\n",
-    "viewer.add_image(im_all[3,], name='YAP/TAZ', colormap='yellow')"
+    "viewer.add_image(im_all[0,], name='nuclei', colormap='cyan', blending='additive')\n",
+    "viewer.add_image(im_all[1,], name='tubulin', colormap='magenta', blending='additive')\n",
+    "viewer.add_image(im_all[2,], name='actin', colormap='green', blending='additive')\n",
+    "viewer.add_image(im_all[3,], name='YAP/TAZ', colormap='yellow', blending='additive')"
    ]
   },
   {
@@ -195,25 +195,25 @@
    },
    "outputs": [],
    "source": [
-    "viewer.add_image(im_gauss, name='nuclei_gaussian_filter')\n",
-    "viewer.add_image(im_thresh, name='nuclei_binary')\n",
-    "viewer.add_labels(labels, name='nuclei_labels')"
+    "viewer.add_image(im_gauss, name='nuclei_gaussian_filter', blending='additive')\n",
+    "viewer.add_image(im_thresh, name='nuclei_binary', blending='additive')\n",
+    "viewer.add_labels(labels, name='nuclei_labels', blending='additive')"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "42b1e9f3-9068-4be8-bc88-0e4bf414425c",
    "metadata": {},
    "source": [
-    "### Import 3D data with `aicsimageio`"
+    "### Import 3D data with `bioio`"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "ad34e423-dbfc-4d61-8a4b-8643f4c84563",
    "metadata": {},
    "source": [
-    "`aicsimageio` is a library for image reading, metadata conversion, and image writing for microscopy images. You can find the full API at [this link](https://allencellmodeling.github.io/aicsimageio/)."
+    "`bioio` is a library for image reading, metadata conversion, and image writing for microscopy images. You can find the full API at [this link](https://bioio-devs.github.io/bioio/)."
    ]
   },
   {
@@ -225,8 +225,8 @@
    },
    "outputs": [],
    "source": [
-    "# read .tif file with Bioformats importer `aicsimageio`\n",
-    "im1_read = AICSImage('../../Data/others/3D_Image.ome.tiff')"
+    "# read .tif file with BioIO importer `bioio`\n",
+    "im1_read = BioImage('../../Data/others/3D_Image.ome.tiff')"
    ]
   },
   {
@@ -303,8 +303,8 @@
    "outputs": [],
    "source": [
     "viewer = napari.Viewer()\n",
-    "viewer.add_image(im1_read.data[0,0,], name='nuclei', colormap='green', scale = scale_um)\n",
-    "viewer.add_image(im1_read.data[0,1,], name='membrane', colormap='magenta', scale = scale_um)"
+    "viewer.add_image(im1_read.data[0,0,], name='nuclei', colormap='green', scale=scale_um, blending='additive')\n",
+    "viewer.add_image(im1_read.data[0,1,], name='membrane', colormap='magenta', scale=scale_um, blending='additive')"
    ]
   },
   {
@@ -323,8 +323,8 @@
    "outputs": [],
    "source": [
     "viewer = napari.Viewer()\n",
-    "viewer.add_image(im1_read_io[:,0,], name='nuclei', colormap='green')\n",
-    "viewer.add_image(im1_read_io[:,1,], name='membrane', colormap='magenta')"
+    "viewer.add_image(im1_read_io[:,0,], name='nuclei', colormap='green', blending='additive')\n",
+    "viewer.add_image(im1_read_io[:,1,], name='membrane', colormap='magenta', blending='additive')"
    ]
   },
   {
@@ -353,7 +353,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.9.20"
   }
  },
  "nbformat": 4,