MicroManager times out with Perfect Focus during time lapse

We are using MicroManager 2.0 to control a Nikon Ti for multi-position time-lapse experiments. Fairly frequently we find that MicroManager quits at some point during the experiment. This has mostly been at night so we were unable to diagnose the cause but yesterday it happened during the day and we saw the following error message:

Error in device “TiPFSStatus” PFS focusing timed out (timeout set to 5000 ms) (25001)

Yet the cells were still in focus.

Can anyone advise?



Hi Jonathan,

How did Micro-Manager “quit” afterwards? Stop responding to user input, or disappear from the screen alltogether?

I am trying to pinpoint issues on several systems with Nikon Ti that seem to come down to occur with certain combinations of Nikon Ti driver and firmware. It would be really beneficial if you could start Help > report a Problem, set it up to log, then run until the error occurs. Even if Micro-Manager crashes, it should offer you to finish the report on restart of MM. Send it (it will get to me), and I can at least add your system as a datapoint in the spreadsheet I plan to make to pinpoint the problem (and hopefully find a fully working combination of driver and firmware).

Thank you, Nico. Previously, MicroManager just disappeared from the screen; this is the first time we caught an error message.

I will set up ‘report a Problem’ next week.


Hi Nico, we have a problem reporting problems to you due to the firewall at our institute. Can I FTP (or similar) the reports to you? They are 148 and 250 MB. Thanks for your help.

Here is the start of the first report:

#Report Format Version: 2.1
#User Name: Catherine Coates
#Organization: ICR
#User e-mail: catherine.coates@icr.ac.uk
#User Description:
| Crashed after 417 frames - ‘error in device TIPFSStatus. PFS focusing timed out (timeout set to 5000ms) (25001)’
#MAC: e4-54-e8-8b-f9-f8
#Host: 30171CMBDT
#User: nikon
#Pid: 12460
#Starting Config File: C:\Users\nikon\Desktop\Flash 4 + Ti + OptoLED.cfg
#Config Changed: no
***** BEGIN Starting Config (C:\Users\nikon\Desktop\Flash 4 + Ti + OptoLED.cfg) *****

Generated by Configurator on Tue Apr 13 18:46:49 BST 2021

and here is the second:

#Report Format Version: 2.1
#User Name: Catherine Coates/Jon Pines
#Organization: ICR
#User e-mail: catherine.coates@icr.ac.uk
#User Description:
| 'Error failed to load hardware configuration. Line 61: Property,Core,Initialize,1
| Error in device 'ITCondenderCassette"
#MAC: e4-54-e8-8b-fa-4d
#Host: 30172CMBDT
#User: nikon
#Pid: 10892
#Starting Config File: C:\Users\nikon\Desktop\NikonTiProfiles\Flash 4 + Ti+ OptoLED.cfg
#Config Changed: yes
#Ending Configuration File: null
***** BEGIN Starting Config (C:\Users\nikon\Desktop\NikonTiProfiles\Flash 4 + Ti+ OptoLED.cfg) *****

Generated by Configurator on Wed Apr 07 17:17:38 BST 2021

Yes, sharing on dropbox or something similar may work around this (not sure what the size limit of image.sc file upload is, you could try;).

I will be looking for versions of the Nikon code: Driver (micUSB), Nikon software, Firmware TiE, and for evidence of problems with the PFS (search for “Error”, and or “TIPFSStatus” and looks for sign of problems.

Coincidentally, it seems that folks back in our lab are running into the same (or similar) problem, and since it takes so long to reproduce it will be very difficult to figure out the root cause.

Micro-Manager disappearing from the screen indicates an “uncaught exception”. Those invariably arise in the lower, device interface layers, i.e. in the Nikon Ti Micro-Manager device adapter code, or in the Nikon software that sits between Micro-Manager and the actual microscope. Having a guaranteed protocol to induce the problem would help enormously finding the root problem.