# ImageJ and Fiji on a Mac: install, Apple Silicon and "can't be opened" fixes

> Download ImageJ or Fiji for Mac (Apple Silicon or Intel), fix "can't be opened" and "damaged" errors, set the memory, and the no-install option.

Published 2026-11-06 by LabCanvas team. https://www.labcanvas.com/blog/imagej-mac

![ImageJ 1.54f main window with Edit › Options › Memory & Threads open: Maximum memory in MB and Parallel threads outlined, and the status bar showing the ImageJ and Java versions](https://www.labcanvas.com/blog/imagej/imagej-mac-memory-threads.webp)

To get ImageJ on a Mac, download **Fiji Latest** from the Fiji download page: **macOS arm64** for Apple Silicon (M1 to M4), **macOS x86-64** for an Intel Mac. Unzip it, drag **Fiji.app** into **Applications** and double-click it; Java 21 is included. If macOS says the app "can't be opened", go to **System Settings › Privacy & Security** and click **Open Anyway**; if it says the app is "damaged", remove the quarantine flag with **xattr -dr com.apple.quarantine /Applications/Fiji.app** in Terminal.

*Checked in November 2026 against the Fiji download page, Fiji's launcher documentation and Apple's Mac User Guide. Download pages change; the official one is imagej.net/software/fiji/downloads.*

## Which download for your Mac

First find your chip: **Apple menu › About This Mac**. "Chip: Apple M…" means Apple Silicon; "Processor: … Intel" means Intel.

| Download | Mac | Java | Choose it when |
|---|---|---|---|
| **Fiji Latest, macOS arm64** (fiji-latest-macos-arm64-jdk.zip) | Apple Silicon, macOS 11 Big Sur or later | Java 21, included | Almost always on an M-series Mac; the Fiji team recommends Latest for most users |
| **Fiji Latest, macOS x86-64** (fiji-latest-macos64-jdk.zip) | Intel, macOS 11 or later | Java 21, included | An Intel Mac |
| **Fiji Stable, macOS x86-64** (fiji-stable-macosx-jdk.zip) | Intel; on Apple Silicon only through Rosetta | Java 8, included | You need Java 8, an older macOS, or an old plugin that breaks on Java 21 |
| **Portable (no JDK)** | Any | Bring your own Java 21 (Latest) or Java 8 (Stable) | Managed machines where Java is installed centrally |
| **ImageJ 1.x** (imagej.net/ij/download.html) | Bundles for Intel (with Java 8) and for Apple Silicon (with Zulu OpenJDK 13) | Included | You want plain ImageJ without Fiji's plugins |

Each Fiji download is offered from three servers (US, UK and France); they hold the same files.

Fiji or plain ImageJ? Fiji is ImageJ with plugins installed and kept up to date: Bio-Formats for .czi, .nd2 and .lif files, TrackMate, Cell Counter, Coloc 2 and many more. Most people should take Fiji; see [Fiji vs ImageJ](https://www.labcanvas.com/blog/fiji-vs-imagej).

## How to install Fiji on a Mac, step by step

1. **Download** the right zip from imagej.net/software/fiji/downloads.
2. **Unzip it** by double-clicking the file in Finder. You get **Fiji.app**.
3. **Drag Fiji.app into Applications.** Do this before you open it the first time (see "Fiji runs from a strange place" below for why).
4. **Open it**: double-click Fiji.app in Applications. The first start takes a little longer. If macOS stops you, go to the fixes below.
5. **Update it**: **Help › Update…** runs the Fiji Updater, which fetches fixes and lets you add update sites (extra plugin collections). Restart when it asks.

Fiji is a portable application: there is no installer. Its plugins, macros and launcher settings live inside Fiji.app; ImageJ's own preferences go in a small file, IJ_Prefs.txt, in your user Library › Preferences folder. To uninstall, drag Fiji.app to the Bin. To see the folders inside, right-click Fiji.app and choose **Show Package Contents**, where you find the **plugins** and **macros** folders.

## "Fiji.app can't be opened": the Gatekeeper fix

Gatekeeper is the part of macOS that checks downloaded apps before they run. When it cannot confirm an app, you see a message such as "Fiji.app can't be opened because Apple cannot check it for malicious software", or "Fiji.app was blocked to protect your Mac".

Apple's own steps:

1. Try to open Fiji.app once and close the message (this records the attempt).
2. Open **Apple menu › System Settings**, click **Privacy & Security** in the sidebar and scroll down to **Security**.
3. Next to the message about Fiji.app, click **Open Anyway** (on some versions **Open**, then **Open Anyway**).
4. Enter your login password when asked. From then on, Fiji opens normally.

On macOS 14 and earlier, Control-clicking the app and choosing **Open** also worked. Since macOS Sequoia (15), that shortcut no longer gets past the warning, so use System Settings.

## "Fiji.app is damaged and can't be opened": the quarantine fix

This message rarely means the download is broken. macOS adds a **quarantine attribute** (com.apple.quarantine) to every file that comes from a browser, and an app that is not notarised can then be reported as "damaged". Removing the attribute from that one app fixes it.

1. Make sure Fiji.app is in **Applications** and came from the official download page.
2. Open **Terminal** (Applications › Utilities).
3. Type, then press Return:

```
xattr -dr com.apple.quarantine /Applications/Fiji.app
```

4. If it answers "Permission denied", run it with **sudo** in front and type your password: `sudo xattr -dr com.apple.quarantine /Applications/Fiji.app`.
5. Open Fiji.app again.

The `-d` flag deletes the attribute and `-r` does it for every file inside the app. Fiji's own source repository contains a script, config/fix-app.sh, that runs the same command (plus a `chflags` to clear locked files); its comment says it exists to convince Gatekeeper that Fiji is fine to run. Do not turn Gatekeeper off for the whole Mac (`spctl --master-disable`): fixing the one app is enough.

## Fiji runs from a strange place, cannot update or forgets its memory

If you open an app straight from the Downloads folder or from inside the zip, macOS may run it from a hidden, random, read-only copy. Apple calls this App Translocation; the ImageJ install page calls it path randomisation. The symptoms: the Updater cannot write its updates, the memory setting is not saved, or plugins you add do not appear.

The fix: quit Fiji, drag Fiji.app into Applications (or any other folder, and back), and open it from there. The ImageJ 1.x install page gives the same advice: dragging ImageJ.app to another folder and (optionally) back turns path randomisation off.

## Nothing happens when I double-click Fiji

Start it from Terminal, where errors are printed instead of hidden. The launcher is a script called **fiji** inside Fiji.app:

```
cd /Applications/Fiji.app
./fiji --debug
```

Read the last lines: a quarantine or permission error points to the fixes above; a Java error usually means a "no JDK" download without the right Java (21 for Fiji Latest). `./fiji --help` lists the other options. If you still use an old Fiji from before 2025 (with the older launcher, Contents/MacOS/ImageJ-macosx), download a fresh Fiji Latest instead of repairing it.

## How much memory to give ImageJ or Fiji on a Mac

ImageJ can only use the memory Java was given when it started, however much RAM the Mac has. A 2 GB stack in a program limited to 2 GB fails with an "out of memory" message.

- **Fiji Latest** starts with **75% of your RAM** by default (the launcher's max-heap setting), which suits most people.
- To change it, use **Edit › Options › Memory & Threads…**, type **Maximum memory** in MB, click OK and restart. In Fiji this writes the max-heap setting into config/jaunch/fiji.cfg inside Fiji.app.
- For one session only, start Fiji from Terminal with `./fiji --mem=8g`.
- **Parallel threads** sets how many processor cores filters and plugins may use; the number of cores is right.

![ImageJ Memory and Threads dialog with Maximum memory and Parallel threads fields, under the ImageJ main window](https://www.labcanvas.com/blog/imagej/imagej-mac-memory-threads.webp "Plain ImageJ 1.54f: Edit › Options › Memory & Threads. Maximum memory in MB 1: on a 16 GB Mac, about 12,000 is 75%. Parallel threads 2: the number of cores. Clicking the status bar 3 shows the version, the Java and the memory in use.")

Keep the maximum below about three quarters of the RAM, so that macOS and your other apps keep enough. Click the ImageJ status bar at any time to see how much memory is in use; with **Run garbage collector on status bar click** ticked, the click also frees memory that is no longer needed.

## How to use ImageJ on a Mac: what is different

- **The menu bar sits at the top of the screen**, like every Mac app, not on the ImageJ window. Click the ImageJ toolbar window to bring its menus back.
- **Command instead of Control** for keyboard shortcuts in ImageJ 1.x: Command O opens, Command M measures, Command Shift P opens Image › Properties.
- **Right-click** is Control-click or a two-finger click on the trackpad (for example on the point tool to pick the Multi-point tool).
- **Keep ImageJ in front during long jobs.** macOS App Nap slows apps that are in the background, and a long macro can crawl while you read e-mail.

![The ImageJ main window: menu bar and toolbar](https://www.labcanvas.com/blog/imagej/ij-main.webp "The ImageJ window: the menus File, Edit, Image, Process, Analyze, Plugins, Window, Help, the toolbar with the selection, line, point, wand, text and zoom tools, and the status bar.")

From here, the everyday jobs are the same as on any computer: [setting the scale](https://www.labcanvas.com/blog/imagej-scale-bar-set-scale), [measuring length and area](https://www.labcanvas.com/blog/measure-length-area-imagej), [counting cells](https://www.labcanvas.com/blog/count-cells-imagej) and the rest in [how to use ImageJ](https://www.labcanvas.com/blog/how-to-use-imagej).

## Pitfalls

- **The wrong build.** Fiji Stable on an M-series Mac runs through Rosetta, more slowly and with Java 8. Unless a plugin needs it, use Fiji Latest arm64.
- **Two Fijis.** An old Fiji.app in Applications and a new one in Downloads: you update one and start the other. Keep one copy.
- **Installing Java separately.** Fiji Latest uses its own Java 21; an Oracle Java you installed for something else is not used and does not help.
- **Disabling Gatekeeper globally.** Not needed: Open Anyway or the xattr command fixes Fiji alone.
- **Unofficial download sites.** Mirrors and "free download" pages sometimes bundle adware or old versions. Use imagej.net (or its UK and French mirrors linked from the download page).

## Citing it

ImageJ and Fiji are free, but cite them in your methods: Schneider et al. (2012) for ImageJ, Schindelin et al. (2012) for Fiji, with the version from **Help › About ImageJ**. The [how to cite ImageJ](https://www.labcanvas.com/blog/how-to-cite-imagej) page has the full references and methods sentences to copy.

## An easier way: measure on a Mac with nothing to install, in LabCanvas

If you only need to measure a few images, or you are on a managed Mac where you cannot approve apps, [LabCanvas Image Analysis](https://www.labcanvas.com/analysis.html) runs in Safari, Chrome or Firefox with no download, no Gatekeeper prompt and no Java. It works the same on an Intel or Apple Silicon Mac, and on an iPad.

1. Open [Image Analysis](https://www.labcanvas.com/analysis.html) in your browser and sign in with a LabCanvas account.
2. Drag a TIFF, PNG or JPEG onto the page, or pick a sample on the start screen. The pixel size is read from ImageJ and OME-TIFF files.
3. Do the job in its tab: **Measure** for lengths, areas and intensities, **Count** › **Count particles** for Analyze Particles with watershed, **Blots** for western blot lanes.
4. Click **Send to Graphs** to plot the results with statistics, or **Copy** to paste them elsewhere.

:::grid
![Image Analysis on an iPad-sized touch screen in LabCanvas Image Analysis](https://www.labcanvas.com/analysis-examples/ipad.webp "Image Analysis on an iPad-sized touch screen: The Nuclei sample on an iPad-sized touch screen 1080 × 810, landscape, counted with a tap on Find nuclei: 70 nuclei, mean area 40.47 µm².")
![Counting nuclei in LabCanvas Image Analysis](https://www.labcanvas.com/analysis-examples/nuclei.webp "Counting nuclei: 70 nuclei counted Otsu threshold, watershed to split touching ones: mean area 40.47 µm², 10.2% of the field.")
![Image check in LabCanvas Image Analysis](https://www.labcanvas.com/analysis-examples/check.webp "Image check: All fine: nothing clipped brightest value 3,688, even illumination the background varies by 1.06×, sharpest at slice 8 of 15.")
:::

Why it is a good choice on a Mac:

- **Nothing to install or unblock**: no quarantine flag, no memory setting, and it runs on any computer or tablet.
- **ImageJ's names and measurements**: an ROI list with Measure and Set measurements, Analyze Particles, the sixteen automatic threshold methods, rolling-ball background, Z Project and Find Maxima.
- **An image check** that flags saturation, JPEG compression and uneven light before you measure.
- **Free with a LabCanvas account** (downloading files is part of LabCanvas Pro), with every measurement checked in [more than 4,000 automated tests](https://www.labcanvas.com/image-analysis-validation).

It does not replace Fiji everywhere: there is no macro language or plugin system, no 3D object analysis or deep-learning segmentation, and vendor files (.czi, .nd2, .lif) need exporting as OME-TIFF first. For those, install Fiji as above. [Open Image Analysis](https://www.labcanvas.com/analysis.html), or read the [complete guide](https://www.labcanvas.com/blog/image-analysis-complete-guide).

ImageJ and Fiji are independent open-source projects; LabCanvas is not affiliated with them.

## References

- Schindelin J, Arganda-Carreras I, Frise E, et al. (2012). Fiji: an open-source platform for biological-image analysis. *Nature Methods* 9, 676–682. [doi:10.1038/nmeth.2019](https://doi.org/10.1038/nmeth.2019)
- Schneider CA, Rasband WS, Eliceiri KW (2012). NIH Image to ImageJ: 25 years of image analysis. *Nature Methods* 9, 671–675. [doi:10.1038/nmeth.2089](https://doi.org/10.1038/nmeth.2089)

## Frequently asked questions

### Which Fiji should I download for an M1, M2, M3 or M4 Mac?

Fiji Latest for macOS arm64 (the file fiji-latest-macos-arm64-jdk.zip on the Fiji download page). It runs natively on Apple Silicon and includes its own Java 21, so you do not need to install Java. Fiji Stable exists only for Intel Macs and runs on Apple Silicon through Rosetta; choose it only if you need Java 8 or an old plugin.

### How do I fix "Fiji.app can't be opened" on a Mac?

Try to open Fiji once, then go to Apple menu › System Settings › Privacy & Security, scroll to Security, click Open Anyway next to the Fiji message and confirm with your password. Since macOS Sequoia (15), Control-clicking the app and choosing Open no longer gets past this warning.

### Fiji says it is damaged and should be moved to the Bin. What do I do?

That message usually comes from the quarantine flag macOS puts on downloaded files, not from real damage. Move Fiji.app to Applications, then in Terminal run: xattr -dr com.apple.quarantine /Applications/Fiji.app (add sudo in front if you get "Permission denied"). Only do this for a copy downloaded from the official Fiji page.

### Do I need to install Java to use ImageJ on a Mac?

No. Fiji Latest ships with Java 21 inside the download, and the ImageJ 1.x downloads for Mac also come bundled with Java. Only the portable "no JDK" download needs a Java runtime you install yourself.

### How do I give ImageJ or Fiji more memory on a Mac?

Edit › Options › Memory & Threads, type the Maximum memory in MB and restart. Fiji already uses 75% of your RAM by default; you can also start it with ./fiji --mem=8g from Terminal. Keep the setting below about three quarters of your RAM.

### Is there an ImageJ app for iPad?

No. ImageJ and Fiji are desktop Java programs that run on macOS, not iPadOS. On an iPad, a browser tool such as LabCanvas Image Analysis (labcanvas.com/analysis.html) covers the everyday jobs: measuring, thresholds, particle counts and blots.

## Related links

- [Install ImageJ or Fiji on Windows 10 and 11](https://www.labcanvas.com/blog/imagej-windows): The same, for PCs
- [Fiji vs ImageJ](https://www.labcanvas.com/blog/fiji-vs-imagej): Which one to download
- [How to use ImageJ](https://www.labcanvas.com/blog/how-to-use-imagej): The ten everyday jobs, step by step
- [ImageJ online](https://www.labcanvas.com/blog/imagej-online): Running ImageJ in a browser
- [Best ImageJ alternatives](https://www.labcanvas.com/blog/imagej-alternatives): Free, online and desktop