diff --git a/Data/Quizzes/Quiz 2/Quiz_2.png b/Data/Quizzes/Quiz 2/Quiz_2.png
new file mode 100644
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diff --git a/Data/Quizzes/Quiz 3/Quiz_3.ome.tif b/Data/Quizzes/Quiz 3/Quiz_3.ome.tif
deleted file mode 100644
index d5734b0..0000000
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diff --git a/Data/Quizzes/Quiz 3/Quiz_3.png b/Data/Quizzes/Quiz 3/Quiz_3.png
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diff --git a/Data/Quizzes/Quiz 1/Quiz_1.czi b/Data/Quizzes/Quiz 4/Quiz_4.czi
similarity index 100%
rename from Data/Quizzes/Quiz 1/Quiz_1.czi
rename to Data/Quizzes/Quiz 4/Quiz_4.czi
diff --git a/Data/Quizzes/Quiz 2/Quiz_2_A.czi b/Data/Quizzes/Quiz 5/Quiz_5_A.czi
similarity index 100%
rename from Data/Quizzes/Quiz 2/Quiz_2_A.czi
rename to Data/Quizzes/Quiz 5/Quiz_5_A.czi
diff --git a/Data/Quizzes/Quiz 2/Quiz_2_B.czi b/Data/Quizzes/Quiz 5/Quiz_5_B.czi
similarity index 100%
rename from Data/Quizzes/Quiz 2/Quiz_2_B.czi
rename to Data/Quizzes/Quiz 5/Quiz_5_B.czi
diff --git a/Data/Quizzes/Quiz 6/Quiz_6.ome.tif b/Data/Quizzes/Quiz 6/Quiz_6.ome.tif
new file mode 100644
index 0000000..8da3a57
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diff --git a/Data/Quizzes/Quiz 4/Quiz_4.ome.tif b/Data/Quizzes/Quiz 7/Quiz_7.ome.tif
similarity index 100%
rename from Data/Quizzes/Quiz 4/Quiz_4.ome.tif
rename to Data/Quizzes/Quiz 7/Quiz_7.ome.tif
diff --git a/Data/Quizzes/Quiz 5/Quiz_5.ome.tif b/Data/Quizzes/Quiz 8/Quiz_8.ome.tif
similarity index 100%
rename from Data/Quizzes/Quiz 5/Quiz_5.ome.tif
rename to Data/Quizzes/Quiz 8/Quiz_8.ome.tif
diff --git a/Pages/Groups.md b/Pages/Groups.md
deleted file mode 100644
index 6e2b689..0000000
--- a/Pages/Groups.md
+++ /dev/null
@@ -1,3 +0,0 @@
-
-| Name | Group |
-|---|---|
diff --git a/Pages/Installation-Instructions.md b/Pages/Installation-Instructions.md
index 633ecf7..517aeb3 100644
--- a/Pages/Installation-Instructions.md
+++ b/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 (David.Barry@crick.ac.uk)
* For conda issues, contact Stefania (stefania.marcotti@kcl.ac.uk)
+## 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/).
diff --git a/README.md b/README.md
index b0726da..3ce5e3c 100644
--- a/README.md
+++ b/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
| 18:00 - ? |
Evening Social |
- TBC |
+ The Lighterman, 3 Granary Square, N1C 4BH |
| Tuesday, October 22nd 2024 |
diff --git a/Scripts/FIJI/Counting.ijm b/Scripts/FIJI/Counting.ijm
index 42acaba..05716fc 100644
--- a/Scripts/FIJI/Counting.ijm
+++ b/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.");
\ No newline at end of file
diff --git a/Scripts/Jupyter/napari_for_visualisation.ipynb b/Scripts/Jupyter/napari_for_visualisation.ipynb
index 7f27df2..f99318b 100644
--- a/Scripts/Jupyter/napari_for_visualisation.ipynb
+++ b/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')"
]
},
{
@@ -195,9 +195,9 @@
},
"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')"
]
},
{
@@ -205,7 +205,7 @@
"id": "42b1e9f3-9068-4be8-bc88-0e4bf414425c",
"metadata": {},
"source": [
- "### Import 3D data with `aicsimageio`"
+ "### Import 3D data with `bioio`"
]
},
{
@@ -213,7 +213,7 @@
"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,