Install BARs with micro-manager

bar
micro-manager
Tags: #<Tag:0x00007fd547b6c988> #<Tag:0x00007fd547b6c2d0>

#1

Hej

I notice that there is someting that allows me to personalise my measuments on ImageJ
but I cannot get it through update if I am using micromanager

This on osx 10 + micromanager 1.4.22
Is there other way to install without going through the Updater?
I am trying to get the “Broadly Applicable Routines.” http://imagej.net/BAR to work or actually I just want something like ROI Manager Tools

Does anyone knows how?


Set different scope objectives in Micro-manger
#2

Raquel,

I guess the easiest way to accomplish all this in the short term, would be to:

  1. Install Fiji (subscribed to the Java8 and BAR update sites) side-by-side with µManager
  2. Symlink the contents of Fiji.app/plugins/ and Fiji.app/macros/tools/ and Fiji.app/macros/toolsets/ to the respective counterparts of the µManager installation

The other alternative is much more convoluted:
You would download the latest jar file and place it in the plugins folder. That would install almost all the scripts and macros of the BAR suite, but not the toolsets such as ROI Manager Tools, which traditionally are not loaded from neither the /plugins directory nor a JAR file but rather from /macros/toolsets/. So you would need to install those manually from GitHub. I guess at this point, even toolsets and macro tools could be bundled within the JAR file, so I opened an issue for it, so it is not forgotten.

Note that without the updater, some dependencies could be missing when running some BAR routines, so you will need to install/symlink them manually ASA you come across a ClassNotFoundException.


#3

But how can I make Fiji to run with micromanger this way?


#4

Sorry Raquel, I do not understand your question. Did you try my suggestion above?
In more detail you will have to:

  1. Install Fiji on your computer. Ensure it is subscribed to the Java 8 & BAR update site. Run the updater to ensure BAR is up-to-date
  2. Install MicroManager on your computer.
  3. Then symlink BAR files from 1) to 2)

The advantage of this approach is that BAR files in MicroManager will always up-to-date when running Fiji’s updater. The disadvantage is, as mentioned, it does not address any missing dependencies.

Here is a script that does the symlinking in step 3) for you. It looks as if you are running MacOS, so I’ve already assumed default installation paths for MacOS:

#!/bin/bash
## IJ BAR: https://github.com/tferr/Scripts#scripts
## Symlinks BAR from a Fiji installation to a MicroManager installation
## http://forum.imagej.net/t/install-bars-with-micro-manager/4524?u=tferr
## Instructions:
## 1. Install Fiji. Ensure it is subscribed to the Java 8 & BAR update site 
## 2. Install MicroManager.
## 3. Edit their respective paths below
## 5. Run the script


## Source and destination paths
FIJI_DIR="/Applications/Fiji.app"
MICROMANAGER_DIR="/Applications/Micro-Manager1.4"

## Symlink files distributed outside the main jar file
for subdir in /macros/tools /macros/toolsets; do
    echo "Symlinking "$subdir
    mkdir -p $MICROMANAGER_DIR$subdir
    ln -fs $FIJI_DIR$subdir/*.ijm $MICROMANAGER_DIR$subdir
done

## Symlink main jar file
echo "Symlinking jar file"
ln -fs $FIJI_DIR/plugins/BAR_*.jar $MICROMANAGER_DIR/plugins

echo "done."

You can run the script above by opening Applications/Utilities/Terminal.app and typing at the prompt:

bash -c '<PASTE THE ABOVE SCRIPT HERE>'

Set different scope objectives in Micro-manger
#5

Thank for the help.

This worked for me