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hardware:troubleshooting [2022/09/22 18:28]
Jon Daniels [Troubles with scanner] |
hardware:troubleshooting [2024/01/19 15:30] (current)
Jon Daniels |
| ===== Troubleshooting ===== | ====== Troubleshooting ====== |
| |
| Try to isolate the problem to the extent possible. | The golden rule of troubleshooting is to bisect the issue until the root cause is clear. Below are some hints. |
| |
| ^ Problem ^ Possible Reason ^ Possible Fix ^ | In case of communication errors between software and hardware, first power cycle the affected hardware and restart the software. If that doesn't resolve things make sure you can communicate with the specific piece of hardware using manufacturer's software (or for Tiger controller, with a serial terminal). |
| | Communication error between software and hardware | | Power cycle the affected hardware and restart the software | | |
| | One hardware element not responding | | Connect to the hardware using manufacturer's software or serial terminal for Tiger controller | | |
| | Beams only come out of the objective if both beams are turned on | Fibers going to the wrong scanner | Exchange the fibers | | |
| | Stage scanning cameras not getting triggered | Hardware/firmware out of date | Make sure you have Rev F XY card or later, make sure micro-mirror card has jumper on positions 11/12 of SV6 | | |
| | Acquisition images look different than alignment (look like epi view) | Camera trigger cables swapped | Swap the camera trigger cables | | |
| | Inconsistent communication with Tiger controller | Windows comm port problems | Update USB to comm port [[http://www.silabs.com/products/mcu/Pages/USBtoUARTBridgeVCPDrivers.aspx|driver (NOT universal version)]], disable USB suspend in Windows per [[https://micro-manager.org/wiki/Personal_computer_setup|Micro-manager recommendations]] | | |
| |
| ==== Piezos ==== | ===== Light Sheet Scanner ===== |
| | |
| | There are two occasional problems people encounter with the scanner, one software-related and the second hardware-related. |
| | |
| | If the beam/sheet seems to disappear or is wildly offset then it is likely the below "beam displaced" software bug. |
| | |
| | If the light sheet scan range is asymmetric or the piezo/slice correspondence is good over part of the scan but not the remainder there may be a damaged MEMS mirror. |
| | |
| | ==== Beam displaced ==== |
| | |
| | On rare occasion the beam disappears because it gets stuck at the edge of its range. This is a software glitch with a straightforward fix. |
| | |
| | Go to the Navigation panel. Depending on the state of the beam/sheet controls the "scanner sheet" axis position should be: |
| | - beam disabled: at 4 degrees (to deflect the beam completely) |
| | - beam is enabled but sheet is disabled: at 0 degrees (if you haven't explicitly changed it) |
| | - beam and sheet both enabled: changing |
| | |
| | In the "beam displaced" situation, when the beam is enabled but the sheet is disabled (middle case0 the "scanner sheet" position will be 4 degrees instead of ~0 degrees. It is resolved by hitting the "go to zero" button in the plugin which moves it back to the normal position, and things should proceed as expected from there. |
| | |
| | If you find a way to reproduce this "beam displaced" situation please contact ASI. We have spent hours in vain trying to figure out what causes this occasional glitch. |
| | |
| | |
| | |
| | ==== Damaged MEMS mirror ==== |
| | |
| | The most common hardware failure of the scanner is when a bit of dust shorts out an actuator on one corner of the MEMS mirror, which is manifest by an asymmetry in scanner. This failure mode seems to be stochastic and can happen after months or years of use without any problem. It requires the MEMS mirror to be replaced by ASI. The damage can occur with either the "slice axis" or "sheet axis". |
| | |
| | A good test is to observe the output position optically as it is moved around the center of its travel. If one side moves more than the other then it is almost certainly a damaged MEMS. |
| | |
| | Observe the beam or sheet optically conjugate to the sample/C-mount. There are a few ways of doing this. One is at the sample with a microscope in epi view and a uniform sample. Another is with the scanner off the microscope and a witness target placed near the C-mount image plane (decent at the outside edge of the scanner, better at the lip at the bottom of the threads, and best 17.5mm inside the outside edge. Another is with the scanner connected to a tube lens and pointed at a wall several meters away. Then move the MEMS from the center position. This can be done either by moving the static position of the beam or else adjusting the amplitude of a continuous movement, either with serial commands or using the plugin. The displacement of the beam should be linear with commaded MEMS deflection, but if one region is strongly attenuated then the MEMS mirror is damaged. |
| | |
| | |
| | ===== Piezos ===== |
| |
| The piezo objective movers are the most fragile and failure-prone component of the diSPIM. See the [[:hardware:piezos|wiki page]] for care and troubleshooting instructions. | The piezo objective movers are the most fragile and failure-prone component of the diSPIM. See the [[:hardware:piezos|wiki page]] for care and troubleshooting instructions. |
| |
| ==== Software ==== | ===== Software ===== |
| | |
| | If you encounter bugs in the Micro-Manager see the [[:software:micro-manager#bug_reports|wiki page]] for reporting instructions. |
| | |
| | ===== Tiger Controller ===== |
| | |
| | If there is inconsistent communication with Tiger controller make sure you have the recommended Windows [[http://www.silabs.com/products/mcu/Pages/USBtoUARTBridgeVCPDrivers.aspx|driver (NOT universal version)]]. |
| | |
| | Also make sure you disable USB suspend in Windows per [[https://micro-manager.org/wiki/Personal_computer_setup|Micro-manager recommendations]]. |
| | |
| | If stage scanning is not getting triggered look at the instructions on the [[:hardware:controller#requirements_for_stage_scanning|page about stage scanning]]. |
| |
| If you encounter bugs in the software it is best to contact the developers directly. For Micro-Manager see the [[:software:micro-manager#bug_reports|wiki page]] for instructions. | |
| |
| ==== Vibration ==== | ===== Vibration ===== |
| |
| Some users have reported vibrations, e.g. diffraction-size beads will appear as a diagonal smear. Assuming you have the system on a floated air table, this is probably due to a combination of the vibration of the camera fan and the "vibration-ability" of the piezo objective movers. The exact threshold of when vibrations become noticeable depends on the experiment specifics. | Some users have reported vibrations, e.g. diffraction-size beads will appear as a diagonal smear. Assuming you have the system on a floated air table, this is probably due to a combination of the vibration of the camera fan and the "vibration-ability" of the piezo objective movers. The exact threshold of when vibrations become noticeable depends on the experiment specifics. |
| - **Reduce susceptibility of piezo to vibrate:** If you have an 2014 or older ASI piezo objective mover you can update to the version introduced early 2015 which is significantly stiffer and hence less prone to vibration. At the same time the mounting scheme was changed which makes alignment significantly easier and offers other minor benefits. The only downside to updating the piezo is that the travel range will be 150 um instead of 300 um. ASI performs such updates at cost, contact them for details. If you are only doing stage scanning the piezos can be eliminated entirely. As of late 2021 ASI offers a bulkier and more expensive piezo objective mover ("s-POM") which is significantly less susceptible to vibration than the standard "f-POM". | - **Reduce susceptibility of piezo to vibrate:** If you have an 2014 or older ASI piezo objective mover you can update to the version introduced early 2015 which is significantly stiffer and hence less prone to vibration. At the same time the mounting scheme was changed which makes alignment significantly easier and offers other minor benefits. The only downside to updating the piezo is that the travel range will be 150 um instead of 300 um. ASI performs such updates at cost, contact them for details. If you are only doing stage scanning the piezos can be eliminated entirely. As of late 2021 ASI offers a bulkier and more expensive piezo objective mover ("s-POM") which is significantly less susceptible to vibration than the standard "f-POM". |
| |
| ==== Out of Bushing Travel ==== | ===== Out of Bushing Travel ===== |
| This process only applies to the 2015 and later piezo mounting scheme. | This process only applies to the 2015 and later piezo mounting scheme. |
| |
| The procedure for the side with the OBLPA is similar but a bit easier. The dovetail is integrated into the OBLPA so it's just a matter of loosening the two bolts that connect it to the piezo, pushing them relative to each other so that its lowest edge will be as close to the XY stage and far from the centerline of the microscope as possible when remounted. Retighten the bolts and reassemble. | The procedure for the side with the OBLPA is similar but a bit easier. The dovetail is integrated into the OBLPA so it's just a matter of loosening the two bolts that connect it to the piezo, pushing them relative to each other so that its lowest edge will be as close to the XY stage and far from the centerline of the microscope as possible when remounted. Retighten the bolts and reassemble. |
| |
| | ===== Wrong Side ===== |
| |
| ==== Troubles with scanner ==== | If the beams only come out of the objective if both beams are turned on then likely fibers going to the wrong scanner and the fibers should be exchanged. |
| |
| There are two occasional problems people encounter with the scanner, one hardware-related and the second software-related. | If acquisition images look like the epi view in live mode instead of the imaging view then the camera trigger cables need to be interchanged. |
| |
| If the light sheet scan is asymmetric or the piezo/slice correspondence is good over part of the scan but not the remainder there may be a damaged MEMS mirror. | |
| |
| If the beam/sheet seems to disappear or is wildly offset while using the Micro-Manager plugin then it could be the below software bug. | |
| |
| === Damaged MEMS mirror === | |
| |
| The most common hardware failure of the scanner is when a bit of dust shorts out an actuator on one corner of the MEMS mirror, which is manifest by an asymmetry in scanner. This failure mode seems to be stochastic and can happen after months or years of use without any problem. It requires the MEMS mirror to be replaced by ASI. The damage can occur with either the "slice axis" or "sheet axis". | |
| |
| A good test is to observe the output position optically as it is moved around the center of its travel. If one side moves more than the other then it is almost certainly a damaged MEMS. | |
| |
| Observe the beam or sheet optically nearly conjugate to the sample/C-mount, either at the sample with a microscope (e.g. the epi view for diSPIM), with the scanner off the microscope and a witness target cut to C-mount size and dropped into the scanner, or else with the scanner connected to a tube lens and then point the beam at a wall many focal lengths away to simulate the far field. Then move the MEMS from the center position (possible to do either by moving the point or adjusting the amplitude of a continuous movement). The MEMS deflection should give a linear displacement, but if one region is strongly attenuated then the MEMS mirror is damaged. | |
| |
| |
| === Plugin confusion === | |
| | |
| Go to the Navigation panel. The "scanner sheet" axis should be at the following places depending on the state: | |
| - beam disabled: at 4 degrees (to deflect the beam completely) | |
| - beam is enabled but not the sheet: at 0 degrees (if you haven't explicitly changed it) | |
| - beam and sheet both enabled: changing | |
| | |
| In the "plugin confused" situation, the middle of these cases will show 4 degrees instead of ~0 degrees. Normally you can fix by hitting the "go to zero" button in the plugin and then moving on. | |
