Use Files from Your Vault or Computer
Let an app take input from your Drylab Vault or straight from your computer, with nuclei counting in DAPI images as the example.
Data lives in different places: some is already in your Vault, some is still on the microscope or instrument computer. Every Drylab app takes files from either place, so nobody has to move data around first.
Why you'd use it
- Data already in Drylab stays put. Pick it from the Vault; nothing is downloaded and uploaded again.
- Data on the instrument PC works too. Upload it from the computer for one run, without adding it to a project first.
- Only the files you choose. An app never reads your Vault on its own. It gets exactly the files you pick, nothing else.
Example: counting nuclei in DAPI images
An imaging core shares a nuclei counter. One user's images are already in their Vault from last week's run; another has a fresh set on the microscope computer. Both use the same app: the first picks the TIFFs from the Vault, the second uploads them.
Prompt to build the app
Build an app that counts nuclei in DAPI images. Let the user pick TIFF images from their vault, or upload them from their computer. Segment the nuclei and split touching ones, show each image with the outlines drawn over it and the count per image, and add a slider for the minimum nucleus area in px² (area in square pixels) so small debris can be left out. Let them exclude an image, then download or save nuclei_counts.csv (image, count, excluded) and the outlined images. Add a Load example button.Percent positive cells:
Extend the app to a second channel: for each nucleus, measure the mean EdU signal and call it positive above a threshold the user sets with a slider. Show percent positive per image and include it in the saved table.Scratch wound assay:
Build an app for scratch wound assays. The user picks a time series of brightfield images from their vault or uploads them. Measure the open wound area in each image, plot percent closure over time, and let them save wound_closure.csv and the plot.How picking and uploading work
Every app shows the same two choices wherever it needs a file:
| Choice | Use it when | What happens |
|---|---|---|
| Pick from Drylab vault | The files are already in Drylab | If you built the app, it opens your Vault directly. Anyone else sees Drylab's "Choose files from your vault", which says "This app is asking for a file. It only receives what you pick." Tick the files and click Use files. |
| Upload from device | The files are on your computer | Your computer's file dialog opens. The files are used for this run. To keep the results, save them. Apps that run Drylab tools keep their inputs and results in their own folder in your Vault. |
You can only choose files of the types the app asked for, such as .tif; other files are greyed out or hidden.
Steps for anyone using the app
- Click Pick from Drylab vault or Upload from device.
- In the vault picker, open the folder, tick the images and click Use files. When the picker opens in its own window, search and the type filter help in large folders.
- Check the outlines, move the minimum area slider until debris is left out, and exclude any out-of-focus image.
- Save the counts. See Save App Results Back to Your Vault.
Tips
- Ask for a file type in the prompt (
.tif,.fastq.gz,.csv), so the picker shows only what fits. - Keep big image sets in the Vault. Picking is faster than uploading the same files every time.
- Give the pixel size in the prompt, so areas can be shown in µm².
Related
Turn an Analysis into a Reusable App
Turn an analysis you've run once, such as RNA-seq differential expression, into an app that reruns the same method on new data.
Save App Results Back to Your Vault
Save what an app produces to your Drylab Vault, not just your laptop, so your next chat can use it, with a qPCR ΔΔCt calculator as the example.