Getting slides onto your computer

What this site is for

There are two different things you might want to do with a slide, and they happen in two different places. Knowing which one you need will save you time.

If you only need to look at slides, you can stop reading here and use the viewer instead. Downloading multi-gigabyte files is rarely worth it just to take a look.

Signing in

Use the same username and password you use for the Digital Slide Archive. This is not a separate account, and there is nothing to register for. If your Archive password changes, it changes here too.

If your account asks for a code

Some accounts have two-factor authentication turned on — the setting that asks for a 6-digit code from an app on your phone. If yours does, here is what to expect:

1. Type your username and password. Leave the 2FA box empty.
2. The page comes back and asks for your code, with your username still filled in. This is normal — it is not an error, and you did not type anything wrong.
3. Open your authenticator app, type the 6 digits, and sign in.

If you don’t use two-factor authentication, ignore that box entirely.

You stay signed in for 12 hours, so you won’t be asked again during a working day. On a shared or public computer, click Sign out when you finish.

Finding your slides

After signing in you’ll see the list of collections. Click one to open it, then keep clicking to move deeper into its folders — the same way folders work on your own computer.

The trail across the top

Shows where you are, like Collections / Collection_Crary_Lab_PSP / PreciseSlides_batch1. Click any part of it to jump straight back to that level. This is usually faster than the browser’s back button.

Filter by name

Start typing in that box and the list narrows to matching names as you type. Useful when a folder holds hundreds of slides and you know part of a case or slide number.

Name, Size, Modified

Click any of these headings to sort by it; click again to reverse. Sorting by Modified is the quickest way to see what was added recently. Folders always stay at the top.

Downloading

Click the Download button next to a file. Your browser saves it the same way it saves anything else — usually straight to your Downloads folder, though your browser may ask where to put it.

The Copy link button does something different: it copies the file’s web address to your clipboard so you can paste it into an email or a message. Whoever receives it will need to sign in themselves — the link is not a way around that.

These files are big

A single whole-slide image is typically 1 to 2 GB, and some run much larger. That is normal for this kind of image, but it has practical consequences:

• Downloads take a while. On a fast connection at the medical center, a slide takes a few minutes. From home, it can take considerably longer. Start it and let it run — you can keep working in other tabs.
• Check you have room. Ten slides can fill 20 GB. Laptops with small drives fill up faster than people expect.
• Downloading many at once is slower, not faster. Three or four at a time is reasonable; twenty will crawl and are more likely to fail.

Opening a slide on your computer

Whole-slide images are not ordinary photographs. They are enormous layered files, and the photo viewer built into Windows or macOS generally cannot open them — if you double-click a slide and nothing happens, or you get an error, that is why. Nothing is wrong with the file.

Use software built for slides instead. QuPath is free, works on Windows and Mac, and is the usual choice for analysis. ImageScope (Windows only) is common for Aperio slides, and most scanner manufacturers ship their own viewer. Ask whoever is supervising your project which one the group uses — it is worth matching them so you can share settings and annotations.

If something goes wrong

The download stopped partway

Open your browser’s downloads list (Ctrl+J on Windows, Cmd+J on a Mac) and look for a Resume option on the interrupted file. It usually picks up where it left off rather than starting over. If it won’t resume, delete the partial file and start again.

It is asking me to sign in again

Sign-ins last 12 hours, so this is expected the next day. Sign in again and carry on — you will land back where you were.

My password isn’t working

This site has no password of its own, so it is your Digital Slide Archive password that is the problem. Confirm it works at crarylabslides.com first. If it doesn’t, reset it there and it will work here.

The slide I want isn’t here

The archive is actively curated, so folders do get reorganized and files renamed. Try the filter box with part of the case number in case it moved. If you still can’t find it, ask the laboratory — don’t assume it was deleted.

I clicked something — did I break anything?

No. This site can only read the archive. Nothing you click here can move, rename, overwrite, or delete a file. Browse freely.

Which site do I need?

The laboratory runs several tools that share the same login. This is the short version of who does what.