CryoTomoSnap

A quick viewer to browse through tomography data with a tagging system to search for data.

NOTE: Using a very simple data structure to browse through dataset, shown in structure.md. Each dataset is a folder containing all the snapshot of each tomogram. The tags for each dataset is stored in imageTags.json in this simple format

{
  "CU428_006": [
    "42kx",
    "round"
  ],
  "CU428_006.png": [
    "42kx",
    "proximal"
  ],
  "CU428_028.png": [
    "42kx",
    "round"
  ]
}

To setup new dataset you can copy directly the folder into /micrographs. If there is no imageTags.json, then imageTags.json (empty) will be created.

---

1. Installation Steps

git clone https://github.com/builab/CryoTomoSnap.git
cd CryoTomoSnap

Initialize a Node.js project:

npm init -y

Install required dependencies:

npm install express cors glob multer

Copy dataset containing images to micrographs to initialize

cp -r /path/to/your/dataset micrographs/

2. Run the Server

Start the server:

node server.js

You should see output like:

Server running on port 3000

3. Access the Application

Open a web browser and navigate to:

http://localhost:3000

4. Access the Application Remotely

SSH Port forwarding

ssh -i -N -f -L localhost:3000:localhost:3000 username@host

Open a web browser and navigate to:

http://localhost:3000

5. Usage

5.1 Main Interface:

You can limit the dataset by name, part of name or tag in the Search box.

5.2 Import a dataset

A dataset is a folder containing the mid-section of your tomogram. For example, all the images of the mid-sections in the warp_tiltseries/reconstruction folder of WarpTools. Alternatively, you can use also segmented snapshot of the tomogram as well.

The interface to import a dataset.

Press "Preview" first and then Import

5.3 Import Tags

You can prepare a csv file in this format

CU428_006, "26kx, proximal"
CU428_028, "26kx, round"
CU428_033, "26kx, round"

Press "Preview" and then "Import". Duplicate tags will not be imported. The name in the csv file can be the exact image name or unique part of the image name.

5.4 Bulk-Tag Dataset

Use this option to tag one or multiple dataset (with wildcard) with the same tag.