Getting started¶

This tour takes one greyscale micro-CT scan from your computer to numbers and figures you can use: upload it, segment it, tidy it up, run a tool from each category, read the results and download them. It takes a few minutes of your time; the jobs run in the cloud while you read their results as they arrive. Each step links to the tool's page in the User guide, which has every setting.

Go to porestore.com and select Sign in. Continue with your Google or GitHub account, or use your email address and password. You land on Home, your team's starting point: from here you can upload images, open your library, run a tool or check on your jobs. Everything you add belongs to your team, so colleagues in it see the same images and results.

PoreStore Home after signing in, with its action cards and recent activity. — Home: start an upload or an operation here, or use Images, Tools and Jobs in the top bar.

2. Upload a 3D image¶

Select Upload, drop a 3D greyscale image on the page (a multi-page TIFF or a NumPy .npy file, for example), give it a name and enter its Voxel size in micrometres. Select Upload. The image appears in your library as processing while PoreStore reads and measures it, then turns ready. You can set or correct the voxel size later; every result follows it. Upload lists every format and its settings.

The Upload page with a greyscale TIFF chosen and its voxel size entered. — Choose the file, give the voxel size if you know it, then select Upload.

3. Segment it into pore and solid¶

Open Tools, select Basic Thresholding under Segmentation, and choose the new image. The page previews one slice of the result as you go: try Otsu first, drag the divider to compare the scan with its segmentation, and check the slice porosity under the preview. Select Run, and PoreStore saves a new binary image beside the greyscale one, with pore as 1 and solid as 0. For a difficult scan, Interactive Segmentation learns from voxels you paint. See Basic Thresholding.

Basic Thresholding previewing an Otsu segmentation of one slice, with a divider comparing it to the scan. — Pick a method, drag the divider to compare, and read the slice porosity below the preview.

4. Trim unwanted edges¶

Scans often include things that aren't sample: the space around a cylindrical core, or a damaged edge. Open Trimming under Preparation and choose the segmented image. Pull the X, Y and Z sliders (or the handles on the preview) in until the box holds only sample, and select Run to save the trimmed copy. See Trimming.

Trimming with the keep-box pulled in on all three cross-sections. — Drag a corner handle or the sliders; each axis shows how many voxels you keep.

5. Clean it¶

Segmentation leaves pores sealed off inside the solid and specks of solid floating in the pores. Open Image Cleaning, choose the trimmed image, tick Fill Invalid Pores and Trim Floating Solid, and select Run. Your image is now ready for any tool. See Image Cleaning.

Image Cleaning with both operations ticked and the new image named. — Tick the operations to run; the panel at the bottom names the image they create.

6. Run a tool from each category¶

Every tool works the same way: choose it, check the image, adjust a setting or two, and select Run. You don't need to wait for one job before starting the next. Here is one from each category; each job runs on its own and lands in Jobs.

Transport: Permeability¶

How easily fluid flows through the sample. Choose Permeability, pick the Flow direction, keep the suggested settings and Backend, and run it. The result gives the permeability in millidarcy and saves the pressure and velocity fields. See Permeability.

The Permeability launch form for the cleaned image. — Choose the flow direction and backend, then select Run.

Structure: Pore Size¶

How big the pores are. Pore Size fits the largest sphere into every part of the pore space and reports the volume-weighted distribution of pore radius, with its median. See Pore Size.

A completed Pore Size job with its pore radius distribution. — The pore radius distribution of a completed Pore Size job.

Statistics: Chord Length¶

Whether the pores are stretched along one axis. Chord Length measures straight runs through the pores along X, Y and Z; different distributions along different axes mean the structure is anisotropic. See Chord Length.

A completed Chord Length job with one distribution per axis. — One chord length curve per axis.

Multiphase: Mercury Porosimetry¶

What a mercury porosimetry test on the sample would show. Mercury Porosimetry pushes a non-wetting fluid in step by step and plots capillary pressure against saturation. See Mercury Porosimetry.

A completed Mercury Porosimetry job with its capillary pressure curves and invasion map. — Intrusion and extrusion curves, and the invasion sequence in the slice viewer.

REV: REV Porosity¶

Whether the sample is big enough to represent the material. REV Porosity measures porosity in many random cubes of growing size; when the scatter settles, the sample is large enough. See REV Porosity.

A completed REV Porosity job with porosity against cube volume. — The scatter narrows as the cubes grow.

Networks: Network Extraction beta¶

A pore network for your own network models. Network Extraction splits the pore space into pores joined by throats and returns the network with every pore's and throat's size and position. See Network Extraction.

A completed Network Extraction job with its pore and throat counts. — The pore and throat counts, and the Pore network file under Available Actions.

Visualize: 3D Visualization¶

See it all in 3D. Once the permeability job has finished, open 3D Visualization, choose the image and select Run. When the viewer is ready, select Open 3D viewer: turn the pore space around, slice through the pressure field, and switch to Flow to see streamlines through the pores. See 3D Visualization.

In progress

Screenshot: the 3D viewer in its browser tab showing the Flow view, streamlines coloured by velocity through the translucent solid. Arrows to the view toggle (Structure, Orthoslices, Flow) and the camera toolbar.

7. Read the results¶

Open Jobs to see every job and its state. While a job waits or runs, its page says so and updates by itself; Job states explains each one. When it completes, the job page shows its tables and charts, and the Jobs list shows the number that sums it up, such as the permeability or the median pore radius. Tools that save 3D fields, such as permeability, show them in a slice viewer: click a point on one slice to move the other two there. Each tool's page in the User guide explains its results.

A completed Permeability job with its headline, results table and velocity field. — The permeability, its convergence checks and the velocity field.

8. Download and export¶

Keep what you need. On any completed job, Download Report gives a PDF or HTML report with its settings, tables and charts, and Download scalar fields saves 3D fields such as velocity or pressure for your own software. To take an image itself elsewhere, Export writes it as VTK image data for ParaView, an STL surface mesh or a NumPy archive. To compare several results, tick them in Jobs and select Export results. See Jobs and results.

The Download Report dialog offering PDF and HTML, beside Download scalar fields. — Download Report offers PDF or HTML; Download scalar fields exports the saved 3D fields.

Where next¶

The User guide has a page for every tool, with all its settings.
The Scientific reference explains what each tool computes, and how.
The Technical reference explains how jobs run and what their states mean.