diff --git a/_includes/auto_threshold/auto_threshold_act1_galaxy.md b/_includes/auto_threshold/auto_threshold_act1_galaxy.md new file mode 100644 index 00000000..9569b13c --- /dev/null +++ b/_includes/auto_threshold/auto_threshold_act1_galaxy.md @@ -0,0 +1,34 @@ +- Navigate to [Galaxy](https://usergalaxy.eu) +- Upload an image + - In the Tools panel on the left side, click `Upload Data`. + - Click the `Paste/Fetch data` button. + - Paste the URLs of the images : [xy_8bit__nuclei_without_offset.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__nuclei_without_offset.tif) and [xy_8bit__nuclei_with_offset.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__nuclei_with_offset.tif) + - Click the `Start` button and wait for the upload to complete. + - Once the upload is finished, click the `Close` button. The image will now be available in your Galaxy history. +- Apply a threshhold + - In the Tools panel on the left side, search `Threshold image`. + - Choose the tool named `Threshold image with scikit-image`, and click on it. + - Manual threshold + - `xy_8bit__nuclei_without_offset.tif` + - Select the image `xy_8bit__nuclei_without_offset.tif` from the `Select image` dropdown list. + - Select `Manual` from the `Thresholding method` dropdown list. + - Set `Threshold value` to `20`. + - Toggle `Invert output labels` to `Yes` + - Click the `Run Tool` button and wait for the job to finish (The job will turn green). + - Click on the job in your Galaxy history to download the resulting image. + - `xy_8bit__nuclei_with_offset.tif` + - Select the image `xy_8bit__nuclei_with_offset.tif` from the `Select image` dropdown list. + - Select `Manual` from the `Thresholding method` dropdown list. + - Set `Threshold value` to `40`. + - Toggle `Invert output labels` to `Yes` + - Click the `Run Tool` button and wait for the job to finish (The job will turn green). + - Click on the job in your Galaxy history to retrieve the results. + - Auto threshold + - `xy_8bit__nuclei_without_offset.tif` + - Select the image `xy_8bit__nuclei_without_offset.tif` from the `Select image` dropdown list. + - Select `Otsu` from the `Thresholding Method` dropdown list. + - Leave `Offset` value unchanged. + - Toggle `Invert output labels` to `Yes` + - Click the `Run Tool` button and wait for the job to finish (The job will turn green). + - Click on the job in your Galaxy history to retrieve the results. + - Repeat the steps for a different image `xy_8bit__nuclei_with_offset.tif` diff --git a/_includes/binarization/binarization_act1_galaxy.md b/_includes/binarization/binarization_act1_galaxy.md new file mode 100644 index 00000000..bfa407cc --- /dev/null +++ b/_includes/binarization/binarization_act1_galaxy.md @@ -0,0 +1,17 @@ +- Navigate to [Galaxy](https://usergalaxy.eu) +- Upload an image + - In the Tools panel on the left side, click `Upload Data`. + - Click the `Paste/Fetch data` button. + - Paste the URLs of the images : [xy_8bit__two_cells.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__two_cells.tif) + - Click the `Start` button and wait for the upload to complete. + - Once the upload is finished, click the `Close` button. The image will now be available in your Galaxy history. +- Apply a threshhold + - In the Tools panel on the left side, search `Threshold image`. + - Choose the tool named `Threshold image with scikit-image`, and click on it. + - Select the image `xy_8bit__two_cells.tif` from the `Select image` dropdown list. + - Select `Manual` from the `Thresholding method` dropdown list. + - Set `Threshold value` to `49`. + - Toggle `Invert output labels` to `Yes` + - Click the `Run Tool` button and wait for the job to finish (The job will turn green). + - Click on the job in your Galaxy history to download the resulting image. + \ No newline at end of file diff --git a/_includes/binarization/binarization_act2_galaxy.md b/_includes/binarization/binarization_act2_galaxy.md new file mode 100644 index 00000000..6600f631 --- /dev/null +++ b/_includes/binarization/binarization_act2_galaxy.md @@ -0,0 +1,17 @@ +- Navigate to [Galaxy](https://usegalaxy.eu) +- Upload an image + - In the Tools panel on the left side, click `Upload Data`. + - Click the `Paste/Fetch data` button. + - Paste the URLs of the images : [xy_8bit__PCNA.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__PCNA.tif) + - Click the `Start` button and wait for the upload to complete. + - Once the upload is finished, click the `Close` button. The image will now be available in your Galaxy history. +- Apply a threshhold + - In the Tools panel on the left side, search `Threshold image`. + - Choose the tool named `Threshold image with scikit-image`, and click on it. + - Select the image `xy_8bit__PCNA.tif` from the `Select image` dropdown list. + - Select `Manual` from the `Thresholding method` dropdown list. + - Experience with different `Threshold value`, e.g. `5`,`44`,`4.5` + - Toggle `Invert output labels` to `Yes` + - Click the `Run Tool` button and wait for the job to finish (The job will turn green). + - Click on the job in your Galaxy history to download the resulting image. + \ No newline at end of file diff --git a/_includes/lut/lut_act1_galaxy.md b/_includes/lut/lut_act1_galaxy.md new file mode 100644 index 00000000..00c25ab4 --- /dev/null +++ b/_includes/lut/lut_act1_galaxy.md @@ -0,0 +1,19 @@ +- Upload an [image](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__nuclei_high_dynamic_range.tif) to Galaxy + - Go to https://usegalaxy.eu + - In the Tools panel on the left, click `Upload Data` + - Click `Paste/Fetch data` button + - Paste the image url: https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__nuclei_high_dynamic_range.tif and click the `Start` button + - Click the `Close` button after upload finishes, then the image will be available in your Galaxy history. +- Start the Napari Interactive Tool + - In the Tools panel on the left, search for `Run Napari interactive tool` + - Select `xy_8bit_nuclei_high_dynamic_range.tif` from the `Images` dropdown list. + - Click the `Run Tool` button. Once the `Open` link appears at the top of the page, click it to open Napari in a separate browser tab. + - In the Napari browser tab, navigate to `File -> Open File(s)` and select the image `xy_8bit_nuclei_high_dynamic_range.tif` from the `input` folder. +- Change the Contrast settings + - Experiment with different minimum and maximum values of the `contract limits`. + - Notice how, at certain settings, a very dim nucleus becomes visible. +- Explore different LUTs, e.g. + - Go to `File › Open File(s)` + - Select the same image `xy_8bit_nuclei_high_dynamic_range.tif` from the `input` folder. A new layer will appear in the bottom left pane. + - Change the `colormap` to `turbo`, from the layer options in the top left pane. + - Turn on grid mode by clicking the `Grid` button located at the bottom left,second from the right. \ No newline at end of file diff --git a/_includes/lut/lut_act2_galaxy.md b/_includes/lut/lut_act2_galaxy.md new file mode 100644 index 00000000..a9cc1ad2 --- /dev/null +++ b/_includes/lut/lut_act2_galaxy.md @@ -0,0 +1,13 @@ +- Upload one of the above pairs of images to Galaxy + - Go to https://usegalaxy.eu + - In the Tools panel on the left, click `Upload Data` + - Click `Paste/Fetch data` button + - Paste the URLs of the two images(one line per URL) and click the `Start` button + - Click the `Close` button after upload finishes, then the image will be available in your Galaxy history. +- Start the Napari interactive tool + - In the Tools panel on the left, search for `Run Napari interactive tool` + - Select the two uploaded images from the `Images` dropdown list + - Click the `Run Tool` button. Once the `Open` link appears at the top of the page, click it to open Napari in a separate browser tab. + - In the Napari tab, navigate to `File -> Open file(s)`, and select the two images from the `input` folder. + - Turn on grid mode by clicking the `Grid` button located at the bottom left,second from the right. The two images will appear side by side + - Adjust the `contrast limits` and apply the same values to both images to compare them directly \ No newline at end of file diff --git a/_includes/median_filter/median_filter_galaxy.md b/_includes/median_filter/median_filter_galaxy.md new file mode 100644 index 00000000..51f95452 --- /dev/null +++ b/_includes/median_filter/median_filter_galaxy.md @@ -0,0 +1,22 @@ +- Upload the following images to Galaxy + - Navigate to [Galaxy](https://usegalaxy.eu) + - Locate the Tools panel on the left, click the `Upload Data` button. + - Within the `Uupload data` pop-up wintow, Click `Paste/Fetch data` button. + - In the text box, paste the URLs of the following images. Enter each URL on a new line. + - [xy_8bit_binary__squares_different_size.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit_binary__squares_different_size.tif) + - [xy_8bit_binary__large_spot.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit_binary__large_spot.tif) + - [xy_8bit__two_noisy_squares_different_size.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit_binary__large_spot.tif) + - [xy_8bit__PCNA.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__PCNA.tif) + - [xy_8bit_binary__test_structures.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit_binary__test_structures.tif) + + - Click the `Start` button to upload the images. + - Once the upload is finished, click the `Close` button at the bottom of the upload window + - The uploaded images will be available in your Galaxy history on the right panel. +- Apply Median Filter + - In the `Tools` panel, search `Filter 2D image`, and click `Filter 2D image with scikit-image` from the search results + - In Galaxy main window,apply the followings + - `Filter type`: `Median` + - `Radius/Sigma`: Explore different values, such as `1`,`2` or `5` + - `Source file`: click the second button to activate `Multiple datasets`. Select images from the dropdown list. + - Click `Run Tool` + - Depending on the number of input images, you will see the corresponding number of outputs in the `History` panel on the right. Wait for them to turn green and download the resulting images. diff --git a/_includes/multichannel_images/activity1_galaxy.md b/_includes/multichannel_images/activity1_galaxy.md new file mode 100644 index 00000000..0edfe352 --- /dev/null +++ b/_includes/multichannel_images/activity1_galaxy.md @@ -0,0 +1,14 @@ +- Upload an [image](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyc_16bit__hela-cells.tif) to Galaxy + - Navigate to [Galaxy]( https://usegalaxy.eu) + - In the Tools panel on the left, click `Upload Data`. + - Click the `Paste/Fetch data` button. + - Paste the image URL: `https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyc_16bit__hela-cells.tif` and click the `Start` button. + - After the upload finishes, click the `Close` button. The image will then be available in your Galaxy history. +- Start the Napari Interactive Tool + - In the Tools panel on the left, search for `Run Napari interactive tool`. + - Select `xyc_16bit__hela-cells.tif` from the `Images` dropdown list. + - Click the `Run Tool` button. + - Once the `Open` link once it appears at the top of the page, click it. This will open Napari in a separate browser tab. + - In the Napari tab, select `File -> Open File(s)`, and choose the image `xyc_16bit__hela-cells.tif` from the "input" folder. The image will be displayed in Napari's main window. + - In the layer pane located at the bottom left, right-click the image and select `Split RGB`. + - Experiment with adjusting the contrast of each channel. diff --git a/_includes/pixels/pixels_act1_galaxy.md b/_includes/pixels/pixels_act1_galaxy.md new file mode 100644 index 00000000..594aa6cd --- /dev/null +++ b/_includes/pixels/pixels_act1_galaxy.md @@ -0,0 +1,17 @@ +## Pixel operation in Galaxy + +- Navigate to [Galaxy](https://usegalaxy.eu) +- In the tools panel on the left, click `Upload Data` +- Click `Paste/Fetch data` button +- Paste the URL of [xy_8bit__nuclei_noisy_different_intensity.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__nuclei_noisy_different_intensity.tif) and click `Start` . +- After the upload finishes, click the `Close` button. The image will then be available in your Galaxy history. +- Pixel operations + - In the `Tools` panel, search for `Operate on pixels with ImageJ2`, and click on it. + - In the main window + - `Select image`: select the image ```xy_8bit__nuclei_noisy_different_intensity.tif``` from the dropdown list. + - `Operation`: Explore different operations from the dropdown list. Refer to the `What it does` section for explainations of each operation. + - `Value`: Some operations requires a value, input corresponding the value. + - Click `Run Tool` to start the operation. + - Results will be available in the Galaxy History panel once the process bar turns green. + + diff --git a/_includes/tool_installation/galaxy.md b/_includes/tool_installation/galaxy.md new file mode 100644 index 00000000..9c1b6f00 --- /dev/null +++ b/_includes/tool_installation/galaxy.md @@ -0,0 +1,3 @@ +