# Software **URL:** https://forum.microlist.org/c/software/11.md?page=1 [Latest](https://forum.microlist.org/latest.md) · [Categories](https://forum.microlist.org/categories.md) · [Tags](https://forum.microlist.org/tags.md) **Page:** 2 --- ## [Using python to control Motor through Serial](https://forum.microlist.org/t/using-python-to-control-motor-through-serial/1667)
**Author:** [@Brian](https://forum.microlist.org/u/Brian)\ **Replies:** 2\ **Last updated:** [August 30, 2023, 6:12pm UTC](https://forum.microlist.org/t/using-python-to-control-motor-through-serial/1667 "2023-08-30T18:12:30Z")
Hi! I was hoping to see if I could get any help in controlling the Cerna MCM3001 (Solld by Thorlabs here: Thorlabs - MCM3001 Three-Channel Controller and Knob Box for 1" Cerna Travel Stages) using serial commands on pyt… --- ## [Open software similar to NIS-Elements AR](https://forum.microlist.org/t/open-software-similar-to-nis-elements-ar/2256)
**Author:** [@BeginnerScope](https://forum.microlist.org/u/BeginnerScope)\ **Replies:** 4\ **Last updated:** [August 25, 2023, 2:39pm UTC](https://forum.microlist.org/t/open-software-similar-to-nis-elements-ar/2256 "2023-08-25T14:39:13Z")
Hello guys, I am a beginner in microscopy and I need to analyse some data from live imaging from a spinning disk scope (BC43). I really like NIS-Elements AR software, where I anaysed some nd2 files as videos basically. … --- ## [Confocal canvas size, Nyquist sampling and FOV](https://forum.microlist.org/t/confocal-canvas-size-nyquist-sampling-and-fov/2248)
**Author:** [@szh141](https://forum.microlist.org/u/szh141)\ **Replies:** 3\ **Last updated:** [August 17, 2023, 9:17pm UTC](https://forum.microlist.org/t/confocal-canvas-size-nyquist-sampling-and-fov/2248 "2023-08-17T21:17:19Z")
Hello all. Can someone shed light on the relationship between canvas size, Nyquist sampling and FOV in confocal microscope? I can calculate the needed pixel size for Nyquist sampling if I know the lens NA, magnification… --- ## [BioImager: Hoping to find people willing to help with development & testing](https://forum.microlist.org/t/bioimager-hoping-to-find-people-willing-to-help-with-development-testing/2226)
**Author:** [@BiologyTools](https://forum.microlist.org/u/BiologyTools)\ **Replies:** 0\ **Last updated:** [July 27, 2023, 11:47am UTC](https://forum.microlist.org/t/bioimager-hoping-to-find-people-willing-to-help-with-development-testing/2226 "2023-07-27T11:47:06Z")
I’m hoping to find people willing to help with development & testing, especially those who have access to hardware. I have been working on an imaging application with .NET6 which supports various microscopes with importe… --- ## [PARD Capture (v1.1) is now available](https://forum.microlist.org/t/pard-capture-v1-1-is-now-available/2185)
**Author:** [@P\_Tadrous](https://forum.microlist.org/u/P_Tadrous)\ **Replies:** 0\ **Last updated:** [May 24, 2023, 8:58am UTC](https://forum.microlist.org/t/pard-capture-v1-1-is-now-available/2185 "2023-05-24T08:58:28Z")
The latest version of (the free and open source) PARD Capture - the standalone image acquisition tool of the PARDUS project - has been released. New features mainly involve upgrades to the live preview. In summary: … --- ## [Adjusting pinhole size per channel on Nikon A1 in Nikon Elements](https://forum.microlist.org/t/adjusting-pinhole-size-per-channel-on-nikon-a1-in-nikon-elements/2134)
**Author:** [@edelaserna](https://forum.microlist.org/u/edelaserna)\ **Replies:** 6\ **Last updated:** [April 25, 2023, 10:29pm UTC](https://forum.microlist.org/t/adjusting-pinhole-size-per-channel-on-nikon-a1-in-nikon-elements/2134 "2023-04-25T22:29:57Z")
Hi everyone, A colleague and I are brainstorming ways to improve his acquisition of a 4-color fixed cell image using AlexaFluor405 (a membrane protein label, not DAPI), AlexaFluor488, AlexaFluor546, and AlexaFluor647 la… --- ## [Shutter control for a Zeiss colibri system](https://forum.microlist.org/t/shutter-control-for-a-zeiss-colibri-system/2070)
**Author:** [@Cyril](https://forum.microlist.org/u/Cyril)\ **Replies:** 1\ **Last updated:** [February 14, 2023, 7:49pm UTC](https://forum.microlist.org/t/shutter-control-for-a-zeiss-colibri-system/2070 "2023-02-14T19:49:13Z")
Hi, I have a Zeiss AxioImager Z1 with two illumination types, a mercury lamp and a Colibri LED system. I control it via MicroManager 2.0. The hardware profile I use has the filters set correctly, and the shutter control … --- ## [Focus map expectations](https://forum.microlist.org/t/focus-map-expectations/2078)
**Author:** [@T\_Usdin](https://forum.microlist.org/u/T_Usdin)\ **Replies:** 0\ **Last updated:** [February 14, 2023, 11:12am UTC](https://forum.microlist.org/t/focus-map-expectations/2078 "2023-02-14T11:12:43Z")
This post is a duplication of one from the Image.sc forum, because it may be more relevant here. I am curious about what is expected for a focus map produced by commercial microscope software and whether there is anythi… --- ## [Nikon elements acquisitions](https://forum.microlist.org/t/nikon-elements-acquisitions/2035)
**Author:** [@Bhuvan](https://forum.microlist.org/u/Bhuvan)\ **Replies:** 2\ **Last updated:** [February 6, 2023, 2:58am UTC](https://forum.microlist.org/t/nikon-elements-acquisitions/2035 "2023-02-06T02:58:27Z")
I am planning to acquire time lapse imaging using Nikon elements 5.3. I need to capture in phase and green fluorescent channel with different time interval between them i.e green channel should be captured at interval of… --- ## [Cross-hair in Live View](https://forum.microlist.org/t/cross-hair-in-live-view/2063)
**Author:** [@simon96c](https://forum.microlist.org/u/simon96c)\ **Replies:** 2\ **Last updated:** [February 4, 2023, 9:34pm UTC](https://forum.microlist.org/t/cross-hair-in-live-view/2063 "2023-02-04T21:34:46Z")
Is anyone aware of any plugins or methods for displaying a crosshair in the Live View? I had a quick look online but couldn’t find anything other than an old post with a broken link. Thanks in advance! --- ## [Scripting in micro-manager2 - how to close acquisition window?](https://forum.microlist.org/t/scripting-in-micro-manager2-how-to-close-acquisition-window/1847)
**Author:** [@pawlowska](https://forum.microlist.org/u/pawlowska)\ **Replies:** 1\ **Last updated:** [January 30, 2023, 4:58am UTC](https://forum.microlist.org/t/scripting-in-micro-manager2-how-to-close-acquisition-window/1847 "2023-01-30T04:58:03Z")
I am running acquisition from script in a loop, changing another device in between\*. At the end, I have tens of acquisition windows open - how to close them from script? It would appear that the current version of the cl… --- ## [USB control of Cairn OptoSpin](https://forum.microlist.org/t/usb-control-of-cairn-optospin/1976)
**Author:** [@carandraug](https://forum.microlist.org/u/carandraug)\ **Replies:** 1\ **Last updated:** [December 4, 2022, 11:35am UTC](https://forum.microlist.org/t/usb-control-of-cairn-optospin/1976 "2022-12-04T11:35:41Z")
I’m trying to control a Cairn OptoSpin 25 filterwheel over USB. The device supports “control via USB” and I did got a document listing the commands from the vendor but that “is the only documentation \[they\] have”. They s… --- ## [New FLOSS for scientific image capture: PARD Capture](https://forum.microlist.org/t/new-floss-for-scientific-image-capture-pard-capture/1955)
**Author:** [@P\_Tadrous](https://forum.microlist.org/u/P_Tadrous)\ **Replies:** 0\ **Last updated:** [November 14, 2022, 1:16am UTC](https://forum.microlist.org/t/new-floss-for-scientific-image-capture-pard-capture/1955 "2022-11-14T01:16:55Z")
This is the first instalment of my PARDUS project. Enjoy. --- ## [Fiji doesn't open .lei files](https://forum.microlist.org/t/fiji-doesnt-open-lei-files/1931)
**Author:** [@Sylvielgki](https://forum.microlist.org/u/Sylvielgki)\ **Replies:** 2\ **Last updated:** [October 7, 2022, 11:25am UTC](https://forum.microlist.org/t/fiji-doesnt-open-lei-files/1931 "2022-10-07T11:25:41Z")
Dear all A user gave me a file acquired on a Leica sp2 ( :no\_mouth:) so it is in the .lei format. I have tried opening it in fiji in many ways but it doesn’t work. I have updates Fiji, ImageJ and all my plugins which in… --- ## [Extreme acquisition slowdown using Nikon NIS Elements AR when doing long term timelapse imaging](https://forum.microlist.org/t/extreme-acquisition-slowdown-using-nikon-nis-elements-ar-when-doing-long-term-timelapse-imaging/1930)
**Author:** [@georgeoshardo](https://forum.microlist.org/u/georgeoshardo)\ **Replies:** 0\ **Last updated:** [October 2, 2022, 9:30am UTC](https://forum.microlist.org/t/extreme-acquisition-slowdown-using-nikon-nis-elements-ar-when-doing-long-term-timelapse-imaging/1930 "2022-10-02T09:30:58Z")
Hi all. We are using a Nikon Ti2-E for long term imaging of bacteria in microfluidic devices. Currently we use Nikon’s proprietary NIS Elements AR software. We have found that during experiments, after maybe 10-12 hours… --- ## [Micromanager Fails to Load Chameleon3 CM3-U3-31S4M](https://forum.microlist.org/t/micromanager-fails-to-load-chameleon3-cm3-u3-31s4m/1926)
**Author:** [@anupam\_bharadwaj](https://forum.microlist.org/u/anupam_bharadwaj)\ **Replies:** 0\ **Last updated:** [September 28, 2022, 6:36am UTC](https://forum.microlist.org/t/micromanager-fails-to-load-chameleon3-cm3-u3-31s4m/1926 "2022-09-28T06:36:20Z")
Micromanager latest version 2.0.0 (july 13, 2021) fails to configure the hardware configuration wizard for the Spinnaker Camera (Chameleon3 CM3-U3-31S4M). During the hardware configuration the Micromanager list modules s… --- ## [Blurring of light sheet](https://forum.microlist.org/t/blurring-of-light-sheet/1892)
**Author:** [@GC\_PENG](https://forum.microlist.org/u/GC_PENG)\ **Replies:** 3\ **Last updated:** [September 13, 2022, 2:34pm UTC](https://forum.microlist.org/t/blurring-of-light-sheet/1892 "2022-09-13T14:34:10Z")
Dear experts, I am a student from China. Recently, when I used the light sheet7 (Zeiss) light microscope to image the pancreatic islets, there was blurring. However, it was very clear during the two-dimensional scanning.… --- ## [μManager 2.0 image window zoom-in behavior](https://forum.microlist.org/t/manager-2-0-image-window-zoom-in-behavior/1915)
**Author:** [@linshao](https://forum.microlist.org/u/linshao)\ **Replies:** 0\ **Last updated:** [September 13, 2022, 2:00pm UTC](https://forum.microlist.org/t/manager-2-0-image-window-zoom-in-behavior/1915 "2022-09-13T14:00:23Z")
Hello, In μManager 2.0, when one zooms in, the image window’s dimensions get bigger and bigger until it fits the entire desktop and blocks the other windows. Is there an option to tell the image window not to enlarge wh… --- ## [Micro Manager fails to load the add Mad City LAbs Nano DRive Z positioning stage](https://forum.microlist.org/t/micro-manager-fails-to-load-the-add-mad-city-labs-nano-drive-z-positioning-stage/1813)
**Author:** [@anupam\_bharadwaj](https://forum.microlist.org/u/anupam_bharadwaj)\ **Replies:** 2\ **Last updated:** [June 10, 2022, 5:55am UTC](https://forum.microlist.org/t/micro-manager-fails-to-load-the-add-mad-city-labs-nano-drive-z-positioning-stage/1813 "2022-06-10T05:55:45Z")
I was trying to run the Mad City Lab Nano Drive - Z100 with the help of Micromanager. However, every time I try to add the MCL Nano Drive Z stage through the Micro Manager it fails. It says, MCL handle error (-8). The nu… --- ## [Micromanager fails to load the Mad City Labs Nano Drive Z stage](https://forum.microlist.org/t/micromanager-fails-to-load-the-mad-city-labs-nano-drive-z-stage/1812)
**Author:** [@anupam\_bharadwaj](https://forum.microlist.org/u/anupam_bharadwaj)\ **Replies:** 2\ **Last updated:** [June 10, 2022, 5:51am UTC](https://forum.microlist.org/t/micromanager-fails-to-load-the-mad-city-labs-nano-drive-z-stage/1812 "2022-06-10T05:51:40Z")
11:23 AM I was trying to run the Mad City Lab Nano Drive - Z100 with the help of Micromanager. However, every time I try to add the MCL Nano Drive Z stage through the Micro Manager it fails. It says, MCL handle error … --- ## [Thorlabs MCM3000 series stage and Basler Camera control software](https://forum.microlist.org/t/thorlabs-mcm3000-series-stage-and-basler-camera-control-software/1649)
**Author:** [@Brian](https://forum.microlist.org/u/Brian)\ **Replies:** 0\ **Last updated:** [December 16, 2021, 9:10pm UTC](https://forum.microlist.org/t/thorlabs-mcm3000-series-stage-and-basler-camera-control-software/1649 "2021-12-16T21:10:12Z")
I was hoping to get some assistance regarding using Micro-Manager to control an MCM3000 Thorlabs Stage Controller (Compact Controllers for Microscopy) and a Basler camera (pylon Open Source). I have search your website … --- ## [Controlling DP26(Olympus) color camera with u-manager](https://forum.microlist.org/t/controlling-dp26-olympus-color-camera-with-u-manager/1603)
**Author:** [@nandan](https://forum.microlist.org/u/nandan)\ **Replies:** 1\ **Last updated:** [November 9, 2021, 12:16am UTC](https://forum.microlist.org/t/controlling-dp26-olympus-color-camera-with-u-manager/1603 "2021-11-09T00:16:55Z")
Hello All, I am trying to control Olympus DP26 camera with u-manager. I don’t see olympus cameras in the list of supported devices, Did anyone try using any DP series cameras with u-manager? If yes, please let me know t… --- ## [Having both Zen Blue and MM on the same system](https://forum.microlist.org/t/having-both-zen-blue-and-mm-on-the-same-system/1554)
**Author:** [@amjad](https://forum.microlist.org/u/amjad)\ **Replies:** 1\ **Last updated:** [October 17, 2021, 7:38am UTC](https://forum.microlist.org/t/having-both-zen-blue-and-mm-on-the-same-system/1554 "2021-10-17T07:38:24Z")
Hi all, I am inheriting a ZEISS LSM710 confocal. Ideally, I want to add a Hamamatsu ORCA-Fusion BT camera on the same scope to use it for both confocal and widefield applications. However, Zen Blue 2.3 (which the highes… --- ## [Microscope manufacturer with best support in Micro-Manager](https://forum.microlist.org/t/microscope-manufacturer-with-best-support-in-micro-manager/1473)
**Author:** [@MPoptik](https://forum.microlist.org/u/MPoptik)\ **Replies:** 2\ **Last updated:** [October 15, 2021, 6:45pm UTC](https://forum.microlist.org/t/microscope-manufacturer-with-best-support-in-micro-manager/1473 "2021-10-15T18:45:02Z")
\[Originally posted on image.sc, from where I was kindly referenced to this forum. Link to original post.\] Hi all, I’m in the process of setting up a new microscopy lab that will use two fully automated epi-fluo systems… --- ## [AiryscanJ and raw airyscan image processing](https://forum.microlist.org/t/airyscanj-and-raw-airyscan-image-processing/1504)
**Author:** [@fadelvalle](https://forum.microlist.org/u/fadelvalle)\ **Replies:** 1\ **Last updated:** [September 18, 2021, 4:40pm UTC](https://forum.microlist.org/t/airyscanj-and-raw-airyscan-image-processing/1504 "2021-09-18T16:40:27Z")
Hi everyone! I was trying the AiryscanJ plugin since I have no place to process raw airyscan images for a long time and I constantly face the out of memory error when applying any of the methods. My pc has 32 GB of ram … --- ## [BigStitcher cannot save as Tiff](https://forum.microlist.org/t/bigstitcher-cannot-save-as-tiff/1481)
**Author:** [@Sylvielgki](https://forum.microlist.org/u/Sylvielgki)\ **Replies:** 2\ **Last updated:** [August 16, 2021, 10:05am UTC](https://forum.microlist.org/t/bigstitcher-cannot-save-as-tiff/1481 "2021-08-16T10:05:30Z")
Dear all We have a light sheet data set of 129GB. We successfully create the xml file and open the data with BigStitcher. We would then like to resave the stitched dataset as Tiff. But when we right click in the tile li… --- ## [Software control of a Thorlabs Nanomax stage](https://forum.microlist.org/t/software-control-of-a-thorlabs-nanomax-stage/1445)
**Author:** [@VroniPfann](https://forum.microlist.org/u/VroniPfann)\ **Replies:** 0\ **Last updated:** [June 22, 2021, 10:57am UTC](https://forum.microlist.org/t/software-control-of-a-thorlabs-nanomax-stage/1445 "2021-06-22T10:57:15Z")
Hi everyone, I would like to control a Thorlabs Nanomax stage at our light sheet microscope using python. I am having troubles with the LoadSettings method from Kinesis as it keeps working unreliably, sometimes it loads… --- ## [Offset and HyD Detectors?](https://forum.microlist.org/t/offset-and-hyd-detectors/1435)
**Author:** [@phoTONIcs](https://forum.microlist.org/u/phoTONIcs)\ **Replies:** 2\ **Last updated:** [June 18, 2021, 5:32pm UTC](https://forum.microlist.org/t/offset-and-hyd-detectors/1435 "2021-06-18T17:32:44Z")
Probably a dumb question… but why is Smart Offset disabled for HyD detectors? If zero values are not good for PMTs, then why are they allowed for HyDs? --- ## [Error message white balance](https://forum.microlist.org/t/error-message-white-balance/1434)
**Author:** [@anne.boehm](https://forum.microlist.org/u/anne.boehm)\ **Replies:** 0\ **Last updated:** [June 10, 2021, 12:53pm UTC](https://forum.microlist.org/t/error-message-white-balance/1434 "2021-06-10T12:53:12Z")
Hi all, I am working with the zeiss microscop and ZEN 2.5 pro programm. I currently have problems with the white balance adjustment and the error message “Set White Balance Interactive (Axio Cam MR Rev3): Image red chan… --- ## [Controlling Olympus SC50 with u-manager](https://forum.microlist.org/t/controlling-olympus-sc50-with-u-manager/1021)
**Author:** [@maznaur](https://forum.microlist.org/u/maznaur)\ **Replies:** 3\ **Last updated:** [January 13, 2021, 3:32pm UTC](https://forum.microlist.org/t/controlling-olympus-sc50-with-u-manager/1021 "2021-01-13T15:32:54Z")
Hi All, I was wondering if someone had a experience controlling the Olympus SC50 camera by micromanager? It doesn’t seem to be listed in the supported device list… Thanks, Mikayel [Previous page](https://forum.microlist.org/c/software/11.md) [Next page](https://forum.microlist.org/c/software/11.md?page=2)