Three analysis station computers
Each one different software
All have ImageJ/Fiji, Microsoft and other programs. You may want to keep your own version of Image/Fiji in your server space as users change the settings on the one here or for version control. (Adobe Suite is not reliably available due to MCIT saving costs by limiting access.)
Sign up in advance at https://nyumc.ilab.agilent.com/sc/4395/microscopy-laboratory/?tab=equipment
Log in with KID and password.
You will automatically be connected to the research-cifs server accessible as drive R:
and to your network home directory accessible as drive H:
You may also have other locations in your profile.
All files should be converted to Imaris format before loading into Imaris. The software is free and installable on 64 bit PC.
Please be aware that file names ending with consecutive numbers may yield unpredictable results. For instance control1, control2, ..., controln. Fix this by changing the number to something else, varying the filename in some other way, or doing the conversions one by one. Imaris support refuses to consider this a bug or to add a checkbox explicitly to treat each file as an individual unit.
In early 2021 Imaris added categorizing features using an "Aritifical Intelligence" interface whereby iterations of automated categorizing and human curation may lead to a robust method for quantification.
If you want to know what is new in Imaris release 9.7:
https://imaris.oxinst.com/learning/view/article/imaris-diving-into-structure-and-dynamics-microscopy-image-analysis (posted 11 Feb 2021)
Core staff are getting more proficient with Imaris and can help you get started. Also, we have access to the experts and highly encourage you to take advantage of this resource. Imaris staff are available by appointment to provide tutorials and problem solving with your data. Please ask core staff how to arrange this.
First time you log in Stations #2 & #3
First time you log in at each computer you need to set up display setting.
Right click on desktop.
Display > Scale and layout > 125% (you may prefer 150%)
To apply the settings, log out and log in.
ANALYSIS STATION #2, Skirball 2nd floor
Imaris As of 18 August 2020 we are running Imaris x64 9.6.0 [Jul 17 2020] Build 55159 for x64
European Patent EP20050009577
Using BisQue, Copyright © 2007-2014, Center for Bio-Image Informatics, University of California, Santa Barbara, CA 93106)
Using Qt, cross-platform application and UI framework, Copyright © 2014 Digia Plc, LGPL v2
Using HDF, data model file format library, Copyright 2006-2015 by the HDF Group, BSD
Using Expat XML Parser, Copyright © 1998, 1999, 2000. Thai Open Source Software Center Ltd and Clark Cooper
Using FFmpeg, multimedia framework, LGPL 2.1
Using FreeImage, graphics image library, FIPL
Using OpenSlide, whole-slide image library, LGPL 2.1
The following notes are MC's personal notes:
How to apply the same surface or spot settings to another image. Or how to continue to train the machine learning on multiple images.
1) Saving creation parameters, including ML classification, are done by click the "magic wand" icon and click "Save parameters for batch". This will create a "favorite" that you can load in STEP1 of the wizard when you open a new image file.
If you saved ML parameters on image#1, start the saved parameters on IMAGE#2, it will used the setting and classify using the saved ML parameters on this image. If you then modify the result by adding to either group and "Retrain" that will add to the existing algorithm.
Then once fully completed, if you save the parameters the added retraining is in the new creation parameters.
How to get an account to set up MatLab:
To get a NetID read all of the steps below and then go to the link in step 1 to be guided through the activation process.
1. You will need to look up your University ID number. Write it down or copy and paste it and save it to use for later: https://library.med.nyu.edu/cgi-bin/university_id_lookup.pl
2. After you login, your University ID will be displayed on the screen. NOTE: copy it down or copy and paste for later.
3. You will then be guided through a series of screens to activate your NetID which will be the same as your Kerberos ID.
4. Your NetID requires a password to be created which can be the same or different as your Kerberos ID. They are on two different systems so they are not in synch with one another.
5. After going through all of the screens, your NetID will be activated and you will also have a new NYU.edu email account which is up to your discretion to use or not use. You would log into NYU.edu email account with your new activated NetID and password.
A complete step by step of the entire process with screen shots can be found here:
Request an unlisted title by clicking here.
MatLab install instructions from within the firewall:
Matlab should already be installed on the computer, but if not https://servicecatalog.nyumc.org/_layouts/15/WopiFrame.aspx?sourcedoc=/Documents/mcit_matlab_installation.pdf&action=default
You need to set up a MatLab account on their website and during the install process, if the license number inthe MCIT instructions doesn't work, back up and setup by choosing the option to use the MatLab account.
last updated 6 Apr 2021
questions, suggestions, etc, please tell us michael.cammer